Mon 24 Dec 07:38:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2okc-2.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2okc-2.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2okc-2.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-parrot-noncs ############### 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 07:39:01 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/noncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-parrot-noncs/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 864 and 0 Target number of residues in the AU: 864 Target solvent content: 0.5257 Checking the provided sequence file Detected sequence length: 445 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 890 Adjusted target solvent content: 0.51 Input MTZ file: 2okc-2.2-parrot-noncs.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: 19 Cell parameters: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-2.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 7120 target number of atoms Had to go as low as 0.55 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 1 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: 28.546 2.200 Wilson plot Bfac: 29.16 46493 reflections ( 91.25 % complete ) and 0 restraints for refining 7834 atoms. Observations/parameters ratio is 1.48 ------------------------------------------------------ Starting model: R = 0.3175 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2723 (Rfree = 0.000) for 7834 atoms. Found 128 (204 requested) and removed 109 (102 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.40 2.37 NCS extension: 0 residues added, 7853 seeds are put forward Round 1: 454 peptides, 82 chains. Longest chain 14 peptides. Score 0.392 Round 2: 553 peptides, 68 chains. Longest chain 30 peptides. Score 0.615 Round 3: 593 peptides, 55 chains. Longest chain 44 peptides. Score 0.719 Round 4: 619 peptides, 47 chains. Longest chain 45 peptides. Score 0.773 Round 5: 647 peptides, 54 chains. Longest chain 50 peptides. Score 0.768 Taking the results from Round 4 Chains 48, Residues 572, Estimated correctness of the model 93.6 % 16 chains (325 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 197 A and 205 A Built loop between residues 265 A and 270 A 44 chains (584 residues) following loop building 13 chains (338 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 11202 restraints for refining 6901 atoms. 7577 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3074 (Rfree = 0.000) for 6901 atoms. Found 152 (180 requested) and removed 106 (90 requested) atoms. Cycle 2: After refmac, R = 0.2833 (Rfree = 0.000) for 6911 atoms. Found 97 (177 requested) and removed 90 (90 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2721 (Rfree = 0.000) for 6880 atoms. Found 79 (173 requested) and removed 81 (90 requested) atoms. Cycle 4: After refmac, R = 0.2611 (Rfree = 0.000) for 6854 atoms. Found 61 (168 requested) and removed 53 (89 requested) atoms. Cycle 5: After refmac, R = 0.2543 (Rfree = 0.000) for 6839 atoms. Found 61 (165 requested) and removed 29 (89 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.29 2.26 NCS extension: 157 residues added (49 deleted due to clashes), 7046 seeds are put forward Round 1: 633 peptides, 47 chains. Longest chain 45 peptides. Score 0.783 Round 2: 674 peptides, 40 chains. Longest chain 64 peptides. Score 0.832 Round 3: 676 peptides, 41 chains. Longest chain 67 peptides. Score 0.831 Round 4: 676 peptides, 41 chains. Longest chain 63 peptides. Score 0.831 Round 5: 682 peptides, 40 chains. Longest chain 60 peptides. Score 0.837 Taking the results from Round 5 Chains 49, Residues 642, Estimated correctness of the model 96.5 % 19 chains (473 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 289 A and 292 A Built loop between residues 315 A and 322 A Built loop between residues 357 A and 360 A Built loop between residues 66 B and 74 B Built loop between residues 146 B and 151 B Built loop between residues 161 B and 165 B Built loop between residues 247 B and 253 B Built loop between residues 264 B and 270 B 38 chains (669 residues) following loop building 11 chains (507 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9208 restraints for refining 6873 atoms. 4549 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2900 (Rfree = 0.000) for 6873 atoms. Found 138 (165 requested) and removed 108 (89 requested) atoms. Cycle 7: After refmac, R = 0.2702 (Rfree = 0.000) for 6889 atoms. Found 86 (162 requested) and removed 90 (90 requested) atoms. Cycle 8: After refmac, R = 0.2584 (Rfree = 0.000) for 6866 atoms. Found 74 (158 requested) and removed 63 (89 requested) atoms. Cycle 9: After refmac, R = 0.2508 (Rfree = 0.000) for 6867 atoms. Found 64 (154 requested) and removed 32 (89 requested) atoms. Cycle 10: After refmac, R = 0.2444 (Rfree = 0.000) for 6891 atoms. Found 55 (155 requested) and removed 32 (90 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.30 2.27 NCS extension: 185 residues added (219 deleted due to clashes), 7112 seeds are put forward Round 1: 692 peptides, 39 chains. Longest chain 63 peptides. Score 0.845 Round 2: 706 peptides, 31 chains. Longest chain 82 peptides. Score 0.873 Round 3: 694 peptides, 33 chains. Longest chain 110 peptides. Score 0.863 Round 4: 700 peptides, 42 chains. Longest chain 65 peptides. Score 0.841 Round 5: 704 peptides, 36 chains. Longest chain 111 peptides. Score 0.859 Taking the results from Round 2 Chains 34, Residues 675, Estimated correctness of the model 97.8 % 13 chains (519 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 B and 70 B Built loop between residues 104 B and 115 B Built loop between residues 144 B and 148 B Built loop between residues 170 B and 173 B Built loop between residues 257 B and 260 B Built loop between residues 375 B and 384 B 25 chains (692 residues) following loop building 7 chains (546 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8970 restraints for refining 7027 atoms. 4016 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2703 (Rfree = 0.000) for 7027 atoms. Found 133 (154 requested) and removed 112 (91 requested) atoms. Cycle 12: After refmac, R = 0.2544 (Rfree = 0.000) for 7036 atoms. Found 72 (151 requested) and removed 93 (92 requested) atoms. Cycle 13: After refmac, R = 0.2440 (Rfree = 0.000) for 7007 atoms. Found 85 (146 requested) and removed 67 (91 requested) atoms. Cycle 14: After refmac, R = 0.2366 (Rfree = 0.000) for 7018 atoms. Found 56 (143 requested) and removed 38 (91 requested) atoms. Cycle 15: After refmac, R = 0.2319 (Rfree = 0.000) for 7028 atoms. Found 57 (139 requested) and removed 37 (91 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.27 2.24 NCS extension: 288 residues added (296 deleted due to clashes), 7347 seeds are put forward Round 1: 701 peptides, 30 chains. Longest chain 69 peptides. Score 0.873 Round 2: 717 peptides, 33 chains. Longest chain 93 peptides. Score 0.873 Round 3: 700 peptides, 38 chains. Longest chain 77 peptides. Score 0.852 Round 4: 704 peptides, 34 chains. Longest chain 71 peptides. Score 0.865 Round 5: 695 peptides, 36 chains. Longest chain 79 peptides. Score 0.855 Taking the results from Round 2 Chains 36, Residues 684, Estimated correctness of the model 97.8 % 13 chains (486 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 186 A and 189 A Built loop between residues 99 B and 109 B Built loop between residues 168 B and 171 B Built loop between residues 229 B and 236 B Built loop between residues 265 B and 269 B 30 chains (701 residues) following loop building 8 chains (508 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9343 restraints for refining 7101 atoms. 4490 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2674 (Rfree = 0.000) for 7101 atoms. Found 134 (137 requested) and removed 111 (92 requested) atoms. Cycle 17: After refmac, R = 0.2514 (Rfree = 0.000) for 7116 atoms. Found 90 (134 requested) and removed 93 (93 requested) atoms. Cycle 18: After refmac, R = 0.2395 (Rfree = 0.000) for 7108 atoms. Found 84 (129 requested) and removed 52 (92 requested) atoms. Cycle 19: After refmac, R = 0.2326 (Rfree = 0.000) for 7133 atoms. Found 76 (126 requested) and removed 28 (93 requested) atoms. Cycle 20: After refmac, R = 0.2272 (Rfree = 0.000) for 7174 atoms. Found 70 (127 requested) and removed 33 (93 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.26 2.23 NCS extension: 270 residues added (224 deleted due to clashes), 7491 seeds are put forward Round 1: 700 peptides, 40 chains. Longest chain 93 peptides. Score 0.846 Round 2: 721 peptides, 27 chains. Longest chain 118 peptides. Score 0.889 Round 3: 710 peptides, 35 chains. Longest chain 80 peptides. Score 0.865 Round 4: 719 peptides, 31 chains. Longest chain 82 peptides. Score 0.879 Round 5: 706 peptides, 38 chains. Longest chain 63 peptides. Score 0.855 Taking the results from Round 2 Chains 30, Residues 694, Estimated correctness of the model 98.3 % 11 chains (554 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 B and 111 B Built loop between residues 168 B and 172 B Built loop between residues 293 B and 296 B Built loop between residues 327 B and 332 B 25 chains (704 residues) following loop building 6 chains (566 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8994 restraints for refining 7211 atoms. 3900 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2595 (Rfree = 0.000) for 7211 atoms. Found 128 (128 requested) and removed 119 (94 requested) atoms. Cycle 22: After refmac, R = 0.2417 (Rfree = 0.000) for 7216 atoms. Found 109 (124 requested) and removed 94 (94 requested) atoms. Cycle 23: After refmac, R = 0.2304 (Rfree = 0.000) for 7227 atoms. Found 92 (120 requested) and removed 61 (94 requested) atoms. Cycle 24: After refmac, R = 0.2253 (Rfree = 0.000) for 7253 atoms. Found 79 (117 requested) and removed 54 (94 requested) atoms. Cycle 25: After refmac, R = 0.2200 (Rfree = 0.000) for 7277 atoms. Found 72 (114 requested) and removed 50 (95 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.25 2.22 NCS extension: 732 residues added (456 deleted due to clashes), 8047 seeds are put forward Round 1: 695 peptides, 38 chains. Longest chain 94 peptides. Score 0.849 Round 2: 730 peptides, 28 chains. Longest chain 112 peptides. Score 0.890 Round 3: 709 peptides, 41 chains. Longest chain 61 peptides. Score 0.848 Round 4: 711 peptides, 36 chains. Longest chain 62 peptides. Score 0.863 Round 5: 699 peptides, 32 chains. Longest chain 89 peptides. Score 0.867 Taking the results from Round 2 Chains 35, Residues 702, Estimated correctness of the model 98.3 % 14 chains (575 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 A and 206 A Built loop between residues 284 A and 287 A Built loop between residues 328 A and 332 A Built loop between residues 168 B and 171 B Built loop between residues 327 B and 330 B 28 chains (718 residues) following loop building 9 chains (594 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8658 restraints for refining 7287 atoms. 3400 conditional restraints added. Observations/parameters ratio is 1.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2508 (Rfree = 0.000) for 7287 atoms. Found 110 (110 requested) and removed 113 (95 requested) atoms. Cycle 27: After refmac, R = 0.2333 (Rfree = 0.000) for 7276 atoms. Found 95 (106 requested) and removed 95 (95 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2256 (Rfree = 0.000) for 7266 atoms. Found 73 (102 requested) and removed 49 (94 requested) atoms. Cycle 29: After refmac, R = 0.2200 (Rfree = 0.000) for 7282 atoms. Found 66 (99 requested) and removed 32 (95 requested) atoms. Cycle 30: After refmac, R = 0.2158 (Rfree = 0.000) for 7311 atoms. Found 49 (99 requested) and removed 36 (95 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.26 2.23 NCS extension: 747 residues added (134 deleted due to clashes), 8078 seeds are put forward Round 1: 714 peptides, 38 chains. Longest chain 93 peptides. Score 0.859 Round 2: 709 peptides, 32 chains. Longest chain 142 peptides. Score 0.872 Round 3: 713 peptides, 38 chains. Longest chain 97 peptides. Score 0.858 Round 4: 714 peptides, 39 chains. Longest chain 63 peptides. Score 0.856 Round 5: 697 peptides, 42 chains. Longest chain 60 peptides. Score 0.839 Taking the results from Round 2 Chains 35, Residues 677, Estimated correctness of the model 97.8 % 12 chains (528 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 179 A and 182 A Built loop between residues 321 B and 324 B 33 chains (681 residues) following loop building 10 chains (532 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9523 restraints for refining 7213 atoms. 4701 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2444 (Rfree = 0.000) for 7213 atoms. Found 94 (94 requested) and removed 105 (94 requested) atoms. Cycle 32: After refmac, R = 0.2322 (Rfree = 0.000) for 7198 atoms. Found 94 (94 requested) and removed 55 (94 requested) atoms. Cycle 33: After refmac, R = 0.2255 (Rfree = 0.000) for 7233 atoms. Found 75 (94 requested) and removed 53 (94 requested) atoms. Cycle 34: After refmac, R = 0.2227 (Rfree = 0.000) for 7249 atoms. Found 89 (94 requested) and removed 50 (94 requested) atoms. Cycle 35: After refmac, R = 0.2205 (Rfree = 0.000) for 7286 atoms. Found 73 (95 requested) and removed 46 (95 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.26 2.23 NCS extension: 206 residues added (90 deleted due to clashes), 7521 seeds are put forward Round 1: 698 peptides, 40 chains. Longest chain 65 peptides. Score 0.845 Round 2: 709 peptides, 32 chains. Longest chain 116 peptides. Score 0.872 Round 3: 689 peptides, 41 chains. Longest chain 61 peptides. Score 0.838 Round 4: 694 peptides, 37 chains. Longest chain 77 peptides. Score 0.852 Round 5: 695 peptides, 40 chains. Longest chain 61 peptides. Score 0.844 Taking the results from Round 2 Chains 37, Residues 677, Estimated correctness of the model 97.8 % 16 chains (549 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 27 A Built loop between residues 156 A and 159 A Built loop between residues 313 A and 316 A Built loop between residues 340 A and 344 A Built loop between residues 233 B and 236 B Built loop between residues 258 B and 262 B 30 chains (690 residues) following loop building 10 chains (563 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8914 restraints for refining 7210 atoms. 3889 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2408 (Rfree = 0.000) for 7210 atoms. Found 94 (94 requested) and removed 104 (94 requested) atoms. Cycle 37: After refmac, R = 0.2281 (Rfree = 0.000) for 7190 atoms. Found 93 (93 requested) and removed 63 (93 requested) atoms. Cycle 38: After refmac, R = 0.2222 (Rfree = 0.000) for 7214 atoms. Found 94 (94 requested) and removed 42 (94 requested) atoms. Cycle 39: After refmac, R = 0.2193 (Rfree = 0.000) for 7261 atoms. Found 73 (94 requested) and removed 45 (94 requested) atoms. Cycle 40: After refmac, R = 0.2166 (Rfree = 0.000) for 7284 atoms. Found 86 (95 requested) and removed 53 (95 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.26 2.23 NCS extension: 595 residues added (279 deleted due to clashes), 7917 seeds are put forward Round 1: 693 peptides, 37 chains. Longest chain 81 peptides. Score 0.851 Round 2: 706 peptides, 30 chains. Longest chain 138 peptides. Score 0.876 Round 3: 697 peptides, 36 chains. Longest chain 90 peptides. Score 0.856 Round 4: 691 peptides, 33 chains. Longest chain 174 peptides. Score 0.861 Round 5: 693 peptides, 42 chains. Longest chain 41 peptides. Score 0.837 Taking the results from Round 2 Chains 34, Residues 676, Estimated correctness of the model 97.9 % 15 chains (562 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 237 A and 240 A Built loop between residues 72 B and 75 B Built loop between residues 150 B and 154 B Built loop between residues 258 B and 261 B Built loop between residues 284 B and 288 B Built loop between residues 375 B and 383 B Built loop between residues 400 B and 407 B 24 chains (696 residues) following loop building 8 chains (587 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8691 restraints for refining 7210 atoms. 3546 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2434 (Rfree = 0.000) for 7210 atoms. Found 94 (94 requested) and removed 108 (94 requested) atoms. Cycle 42: After refmac, R = 0.2301 (Rfree = 0.000) for 7190 atoms. Found 93 (93 requested) and removed 90 (93 requested) atoms. Cycle 43: After refmac, R = 0.2235 (Rfree = 0.000) for 7192 atoms. Found 84 (93 requested) and removed 36 (93 requested) atoms. Cycle 44: After refmac, R = 0.2189 (Rfree = 0.000) for 7238 atoms. Found 73 (94 requested) and removed 33 (94 requested) atoms. Cycle 45: After refmac, R = 0.2147 (Rfree = 0.000) for 7278 atoms. Found 75 (95 requested) and removed 40 (95 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.22 NCS extension: 490 residues added (197 deleted due to clashes), 7814 seeds are put forward Round 1: 696 peptides, 36 chains. Longest chain 118 peptides. Score 0.855 Round 2: 706 peptides, 32 chains. Longest chain 117 peptides. Score 0.871 Round 3: 691 peptides, 35 chains. Longest chain 82 peptides. Score 0.856 Round 4: 665 peptides, 45 chains. Longest chain 81 peptides. Score 0.811 Round 5: 671 peptides, 36 chains. Longest chain 89 peptides. Score 0.843 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 674, Estimated correctness of the model 97.7 % 12 chains (523 residues) have been docked in sequence Sequence coverage is 77 % Consider running further cycles of model building using 2okc-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 41 A and 51 A Built loop between residues 168 A and 172 A Built loop between residues 314 A and 317 A Built loop between residues 369 A and 382 A Built loop between residues 168 B and 171 B Built loop between residues 183 B and 186 B 27 chains (696 residues) following loop building 6 chains (553 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 46493 reflections ( 91.25 % complete ) and 9206 restraints for refining 7335 atoms. 4177 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2509 (Rfree = 0.000) for 7335 atoms. Found 0 (95 requested) and removed 6 (95 requested) atoms. Cycle 47: After refmac, R = 0.2400 (Rfree = 0.000) for 7323 atoms. Found 0 (95 requested) and removed 3 (95 requested) atoms. Cycle 48: After refmac, R = 0.2341 (Rfree = 0.000) for 7319 atoms. Found 0 (95 requested) and removed 5 (95 requested) atoms. Cycle 49: After refmac, R = 0.2311 (Rfree = 0.000) for 7311 atoms. Found 0 (95 requested) and removed 2 (95 requested) atoms. Writing output files ... TimeTaking 88.2