Mon 24 Dec 00:43:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2g0t-2.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-2.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-2.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-2.7-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-2.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-2.7-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:43:20 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-2.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-2.7-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1027 and 0 Target number of residues in the AU: 1027 Target solvent content: 0.5256 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-2.7-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-2.7-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 0.95 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.560 2.670 Wilson plot Bfac: 29.18 34502 reflections ( 99.54 % complete ) and 0 restraints for refining 6167 atoms. Observations/parameters ratio is 1.40 ------------------------------------------------------ Starting model: R = 0.3612 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3146 (Rfree = 0.000) for 6167 atoms. Found 92 (92 requested) and removed 52 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.59 2.02 NCS extension: 0 residues added, 6207 seeds are put forward Round 1: 489 peptides, 68 chains. Longest chain 17 peptides. Score 0.493 Round 2: 542 peptides, 53 chains. Longest chain 37 peptides. Score 0.629 Round 3: 578 peptides, 45 chains. Longest chain 49 peptides. Score 0.697 Round 4: 567 peptides, 44 chains. Longest chain 45 peptides. Score 0.692 Round 5: 571 peptides, 40 chains. Longest chain 43 peptides. Score 0.712 Taking the results from Round 5 Chains 43, Residues 531, Estimated correctness of the model 81.8 % 13 chains (270 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 A and 200 A Built loop between residues 211 A and 219 A Built loop between residues 239 A and 242 A Built loop between residues 263 A and 266 A Built loop between residues 205 B and 215 B Built loop between residues 229 B and 232 B 36 chains (553 residues) following loop building 7 chains (296 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 8386 restraints for refining 5682 atoms. 5072 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3250 (Rfree = 0.000) for 5682 atoms. Found 85 (85 requested) and removed 66 (42 requested) atoms. Cycle 2: After refmac, R = 0.3031 (Rfree = 0.000) for 5626 atoms. Found 83 (83 requested) and removed 52 (42 requested) atoms. Cycle 3: After refmac, R = 0.2900 (Rfree = 0.000) for 5614 atoms. Found 82 (82 requested) and removed 51 (42 requested) atoms. Cycle 4: After refmac, R = 0.2797 (Rfree = 0.000) for 5622 atoms. Found 75 (79 requested) and removed 43 (42 requested) atoms. Cycle 5: After refmac, R = 0.2723 (Rfree = 0.000) for 5624 atoms. Found 77 (78 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.44 1.90 NCS extension: 347 residues added (139 deleted due to clashes), 6014 seeds are put forward Round 1: 580 peptides, 37 chains. Longest chain 108 peptides. Score 0.731 Round 2: 604 peptides, 29 chains. Longest chain 88 peptides. Score 0.777 Round 3: 614 peptides, 26 chains. Longest chain 77 peptides. Score 0.794 Round 4: 610 peptides, 27 chains. Longest chain 80 peptides. Score 0.788 Round 5: 616 peptides, 24 chains. Longest chain 78 peptides. Score 0.802 Taking the results from Round 5 Chains 32, Residues 592, Estimated correctness of the model 90.8 % 17 chains (511 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 36 A Built loop between residues 46 A and 50 A Built loop between residues 94 A and 103 A Built loop between residues 206 A and 212 A Built loop between residues 288 A and 291 A Built loop between residues 31 B and 42 B Built loop between residues 99 B and 105 B Built loop between residues 178 B and 183 B Built loop between residues 207 B and 211 B Built loop between residues 220 B and 227 B Built loop between residues 276 B and 279 B 15 chains (631 residues) following loop building 6 chains (562 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 6201 restraints for refining 5730 atoms. 1588 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2845 (Rfree = 0.000) for 5730 atoms. Found 77 (77 requested) and removed 64 (43 requested) atoms. Cycle 7: After refmac, R = 0.2585 (Rfree = 0.000) for 5706 atoms. Found 76 (76 requested) and removed 47 (43 requested) atoms. Cycle 8: After refmac, R = 0.2432 (Rfree = 0.000) for 5716 atoms. Found 74 (74 requested) and removed 48 (43 requested) atoms. Cycle 9: After refmac, R = 0.2327 (Rfree = 0.000) for 5720 atoms. Found 72 (72 requested) and removed 48 (43 requested) atoms. Cycle 10: After refmac, R = 0.2243 (Rfree = 0.000) for 5729 atoms. Found 71 (71 requested) and removed 46 (43 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.41 1.88 NCS extension: 592 residues added (88 deleted due to clashes), 6366 seeds are put forward Round 1: 616 peptides, 21 chains. Longest chain 155 peptides. Score 0.812 Round 2: 629 peptides, 21 chains. Longest chain 131 peptides. Score 0.819 Round 3: 628 peptides, 21 chains. Longest chain 103 peptides. Score 0.818 Round 4: 625 peptides, 25 chains. Longest chain 115 peptides. Score 0.804 Round 5: 620 peptides, 30 chains. Longest chain 58 peptides. Score 0.784 Taking the results from Round 2 Chains 24, Residues 608, Estimated correctness of the model 92.2 % 17 chains (582 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 129 A and 132 A Built loop between residues 261 A and 265 A Built loop between residues 304 A and 307 A Built loop between residues 319 A and 324 A Built loop between residues 29 B and 40 B Built loop between residues 86 B and 89 B Built loop between residues 99 B and 105 B Built loop between residues 127 B and 135 B Built loop between residues 178 B and 182 B Built loop between residues 206 B and 209 B Built loop between residues 216 B and 219 B 10 chains (645 residues) following loop building 5 chains (626 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 5879 restraints for refining 5718 atoms. 910 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2417 (Rfree = 0.000) for 5718 atoms. Found 68 (68 requested) and removed 62 (42 requested) atoms. Cycle 12: After refmac, R = 0.2136 (Rfree = 0.000) for 5709 atoms. Found 67 (67 requested) and removed 53 (43 requested) atoms. Cycle 13: After refmac, R = 0.2013 (Rfree = 0.000) for 5702 atoms. Found 65 (65 requested) and removed 49 (43 requested) atoms. Cycle 14: After refmac, R = 0.1923 (Rfree = 0.000) for 5708 atoms. Found 63 (63 requested) and removed 45 (42 requested) atoms. Cycle 15: After refmac, R = 0.1856 (Rfree = 0.000) for 5720 atoms. Found 62 (62 requested) and removed 47 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.38 1.85 NCS extension: 53 residues added (103 deleted due to clashes), 5803 seeds are put forward Round 1: 645 peptides, 14 chains. Longest chain 123 peptides. Score 0.848 Round 2: 650 peptides, 16 chains. Longest chain 167 peptides. Score 0.845 Round 3: 654 peptides, 11 chains. Longest chain 193 peptides. Score 0.860 Round 4: 644 peptides, 22 chains. Longest chain 58 peptides. Score 0.824 Round 5: 651 peptides, 20 chains. Longest chain 83 peptides. Score 0.833 Taking the results from Round 3 Chains 11, Residues 643, Estimated correctness of the model 95.1 % 11 chains (643 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 104 A and 107 A Built loop between residues 153 A and 160 A Built loop between residues 213 A and 217 A Built loop between residues 224 A and 227 A Built loop between residues 322 A and 325 A Built loop between residues 61 B and 64 B Built loop between residues 101 B and 105 B Built loop between residues 127 B and 131 B Built loop between residues 153 B and 157 B 2 chains (669 residues) following loop building 2 chains (669 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 5573 restraints for refining 5753 atoms. 317 conditional restraints added. Observations/parameters ratio is 1.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2030 (Rfree = 0.000) for 5753 atoms. Found 60 (60 requested) and removed 52 (43 requested) atoms. Cycle 17: After refmac, R = 0.1845 (Rfree = 0.000) for 5749 atoms. Found 58 (58 requested) and removed 47 (43 requested) atoms. Cycle 18: After refmac, R = 0.1781 (Rfree = 0.000) for 5751 atoms. Found 57 (57 requested) and removed 45 (43 requested) atoms. Cycle 19: After refmac, R = 0.1743 (Rfree = 0.000) for 5758 atoms. Found 55 (55 requested) and removed 46 (43 requested) atoms. Cycle 20: After refmac, R = 0.1725 (Rfree = 0.000) for 5762 atoms. Found 53 (53 requested) and removed 46 (43 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.36 1.84 NCS extension: 1 residues added (2 deleted due to clashes), 5780 seeds are put forward Round 1: 658 peptides, 12 chains. Longest chain 123 peptides. Score 0.859 Round 2: 662 peptides, 12 chains. Longest chain 167 peptides. Score 0.861 Round 3: 664 peptides, 10 chains. Longest chain 141 peptides. Score 0.867 Round 4: 656 peptides, 12 chains. Longest chain 210 peptides. Score 0.858 Round 5: 661 peptides, 16 chains. Longest chain 171 peptides. Score 0.850 Taking the results from Round 3 Chains 12, Residues 654, Estimated correctness of the model 95.6 % 11 chains (653 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A Built loop between residues 99 A and 103 A Built loop between residues 128 A and 132 A Built loop between residues 257 A and 260 A Built loop between residues 306 A and 309 A Built loop between residues 152 B and 156 B Built loop between residues 180 B and 183 B Built loop between residues 322 B and 325 B 3 chains (672 residues) following loop building 3 chains (672 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 5497 restraints for refining 5699 atoms. 215 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1888 (Rfree = 0.000) for 5699 atoms. Found 51 (51 requested) and removed 54 (42 requested) atoms. Cycle 22: After refmac, R = 0.1755 (Rfree = 0.000) for 5690 atoms. Found 49 (49 requested) and removed 47 (42 requested) atoms. Cycle 23: After refmac, R = 0.1708 (Rfree = 0.000) for 5689 atoms. Found 48 (48 requested) and removed 45 (42 requested) atoms. Cycle 24: After refmac, R = 0.1682 (Rfree = 0.000) for 5686 atoms. Found 46 (46 requested) and removed 43 (42 requested) atoms. Cycle 25: After refmac, R = 0.1669 (Rfree = 0.000) for 5687 atoms. Found 44 (44 requested) and removed 43 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.37 1.84 NCS extension: 263 residues added (125 deleted due to clashes), 5962 seeds are put forward Round 1: 669 peptides, 8 chains. Longest chain 279 peptides. Score 0.875 Round 2: 668 peptides, 8 chains. Longest chain 338 peptides. Score 0.874 Round 3: 660 peptides, 12 chains. Longest chain 166 peptides. Score 0.860 Round 4: 664 peptides, 17 chains. Longest chain 164 peptides. Score 0.848 Round 5: 662 peptides, 13 chains. Longest chain 156 peptides. Score 0.858 Taking the results from Round 1 Chains 8, Residues 661, Estimated correctness of the model 96.0 % 7 chains (653 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 28 A and 31 A Built loop between residues 68 A and 72 A Built loop between residues 150 B and 153 B Built loop between residues 321 B and 324 B 4 chains (670 residues) following loop building 3 chains (662 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 5626 restraints for refining 5663 atoms. 394 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1785 (Rfree = 0.000) for 5663 atoms. Found 42 (42 requested) and removed 45 (42 requested) atoms. Cycle 27: After refmac, R = 0.1724 (Rfree = 0.000) for 5655 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1691 (Rfree = 0.000) for 5651 atoms. Found 42 (42 requested) and removed 43 (42 requested) atoms. Cycle 29: After refmac, R = 0.1694 (Rfree = 0.000) for 5646 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 30: After refmac, R = 0.1662 (Rfree = 0.000) for 5644 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.38 1.85 NCS extension: 208 residues added (198 deleted due to clashes), 5853 seeds are put forward Round 1: 654 peptides, 11 chains. Longest chain 165 peptides. Score 0.860 Round 2: 663 peptides, 8 chains. Longest chain 219 peptides. Score 0.872 Round 3: 665 peptides, 10 chains. Longest chain 125 peptides. Score 0.868 Round 4: 653 peptides, 18 chains. Longest chain 116 peptides. Score 0.840 Round 5: 651 peptides, 15 chains. Longest chain 166 peptides. Score 0.848 Taking the results from Round 2 Chains 8, Residues 655, Estimated correctness of the model 95.9 % 7 chains (649 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 33 A Built loop between residues 127 A and 132 A Built loop between residues 69 B and 72 B Built loop between residues 153 B and 158 B Built loop between residues 322 B and 325 B 3 chains (670 residues) following loop building 2 chains (664 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 5634 restraints for refining 5658 atoms. 411 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1855 (Rfree = 0.000) for 5658 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 32: After refmac, R = 0.1746 (Rfree = 0.000) for 5652 atoms. Found 42 (42 requested) and removed 43 (42 requested) atoms. Cycle 33: After refmac, R = 0.1703 (Rfree = 0.000) for 5647 atoms. Found 42 (42 requested) and removed 43 (42 requested) atoms. Cycle 34: After refmac, R = 0.1679 (Rfree = 0.000) for 5645 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 35: After refmac, R = 0.1670 (Rfree = 0.000) for 5642 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.37 1.84 NCS extension: 2 residues added (7 deleted due to clashes), 5648 seeds are put forward Round 1: 657 peptides, 11 chains. Longest chain 141 peptides. Score 0.862 Round 2: 669 peptides, 5 chains. Longest chain 218 peptides. Score 0.882 Round 3: 664 peptides, 11 chains. Longest chain 167 peptides. Score 0.865 Round 4: 656 peptides, 13 chains. Longest chain 219 peptides. Score 0.856 Round 5: 651 peptides, 18 chains. Longest chain 97 peptides. Score 0.839 Taking the results from Round 2 Chains 5, Residues 664, Estimated correctness of the model 96.4 % 5 chains (664 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 A and 158 A Built loop between residues 28 B and 31 B Built loop between residues 128 B and 132 B 2 chains (673 residues) following loop building 2 chains (673 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 5507 restraints for refining 5658 atoms. 216 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1817 (Rfree = 0.000) for 5658 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 37: After refmac, R = 0.1721 (Rfree = 0.000) for 5650 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. Cycle 38: After refmac, R = 0.1679 (Rfree = 0.000) for 5648 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. Cycle 39: After refmac, R = 0.1676 (Rfree = 0.000) for 5646 atoms. Found 42 (42 requested) and removed 43 (42 requested) atoms. Cycle 40: After refmac, R = 0.1666 (Rfree = 0.000) for 5644 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.37 1.84 NCS extension: 0 residues added, 5647 seeds are put forward Round 1: 665 peptides, 10 chains. Longest chain 190 peptides. Score 0.868 Round 2: 670 peptides, 8 chains. Longest chain 208 peptides. Score 0.875 Round 3: 657 peptides, 9 chains. Longest chain 192 peptides. Score 0.867 Round 4: 662 peptides, 11 chains. Longest chain 203 peptides. Score 0.864 Round 5: 660 peptides, 12 chains. Longest chain 263 peptides. Score 0.860 Taking the results from Round 2 Chains 8, Residues 662, Estimated correctness of the model 96.0 % 7 chains (653 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 129 A and 132 A Built loop between residues 180 A and 183 A Built loop between residues 224 A and 227 A Built loop between residues 97 B and 100 B Built loop between residues 306 B and 309 B 3 chains (672 residues) following loop building 2 chains (663 residues) in sequence following loop building ------------------------------------------------------ 34502 reflections ( 99.54 % complete ) and 5606 restraints for refining 5644 atoms. 371 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1819 (Rfree = 0.000) for 5644 atoms. Found 42 (42 requested) and removed 48 (42 requested) atoms. Cycle 42: After refmac, R = 0.1733 (Rfree = 0.000) for 5636 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. Cycle 43: After refmac, R = 0.1702 (Rfree = 0.000) for 5634 atoms. Found 42 (42 requested) and removed 45 (42 requested) atoms. Cycle 44: After refmac, R = 0.1708 (Rfree = 0.000) for 5629 atoms. Found 42 (42 requested) and removed 45 (42 requested) atoms. Cycle 45: After refmac, R = 0.1685 (Rfree = 0.000) for 5624 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.36 1.84 NCS extension: 3 residues added (9 deleted due to clashes), 5630 seeds are put forward Round 1: 658 peptides, 13 chains. Longest chain 115 peptides. Score 0.857 Round 2: 656 peptides, 11 chains. Longest chain 167 peptides. Score 0.861 Round 3: 649 peptides, 12 chains. Longest chain 174 peptides. Score 0.855 Round 4: 655 peptides, 17 chains. Longest chain 127 peptides. Score 0.844 Round 5: 659 peptides, 14 chains. Longest chain 136 peptides. Score 0.854 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 645, Estimated correctness of the model 95.2 % 10 chains (638 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 34 A and 37 A Built loop between residues 60 A and 64 A Built loop between residues 100 A and 103 A Built loop between residues 127 A and 135 A Built loop between residues 153 A and 156 A Built loop between residues 180 A and 183 A Built loop between residues 153 B and 158 B Built loop between residues 321 B and 324 B 3 chains (669 residues) following loop building 2 chains (662 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 34502 reflections ( 99.54 % complete ) and 5216 restraints for refining 5115 atoms. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2392 (Rfree = 0.000) for 5115 atoms. Found 38 (38 requested) and removed 0 (38 requested) atoms. Cycle 47: After refmac, R = 0.2247 (Rfree = 0.000) for 5115 atoms. Found 38 (38 requested) and removed 3 (38 requested) atoms. Cycle 48: After refmac, R = 0.2183 (Rfree = 0.000) for 5115 atoms. Found 39 (39 requested) and removed 2 (39 requested) atoms. Cycle 49: After refmac, R = 0.2123 (Rfree = 0.000) for 5115 atoms. TimeTaking 287.23