null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkz-2.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-2.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-2.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-parrot-hancs/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 777 and 0 Target number of residues in the AU: 777 Target solvent content: 0.5035 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-2.9-parrot-hancs.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: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-2.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.50 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: 19.959 2.900 Wilson plot Bfac: 24.19 17874 reflections ( 95.70 % complete ) and 0 restraints for refining 7324 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.2945 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2205 (Rfree = 0.000) for 7324 atoms. Found 57 (87 requested) and removed 87 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.41 2.51 Search for helices and strands: 0 residues in 0 chains, 7438 seeds are put forward NCS extension: 0 residues added, 7438 seeds are put forward Round 1: 478 peptides, 88 chains. Longest chain 17 peptides. Score 0.417 Round 2: 536 peptides, 74 chains. Longest chain 21 peptides. Score 0.604 Round 3: 549 peptides, 68 chains. Longest chain 21 peptides. Score 0.655 Round 4: 565 peptides, 65 chains. Longest chain 28 peptides. Score 0.690 Round 5: 569 peptides, 57 chains. Longest chain 28 peptides. Score 0.733 Taking the results from Round 5 Chains 65, Residues 512, Estimated correctness of the model 79.4 % 15 chains (219 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 44 A Built loop between residues 109 A and 115 A Built loop between residues 189 A and 197 A Built loop between residues 255 A and 266 A 57 chains (536 residues) following loop building 11 chains (249 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 10091 restraints for refining 6068 atoms. 7009 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2747 (Rfree = 0.000) for 6068 atoms. Found 72 (72 requested) and removed 93 (36 requested) atoms. Cycle 2: After refmac, R = 0.2551 (Rfree = 0.000) for 5978 atoms. Found 47 (70 requested) and removed 44 (35 requested) atoms. Cycle 3: After refmac, R = 0.2447 (Rfree = 0.000) for 5955 atoms. Found 30 (68 requested) and removed 36 (35 requested) atoms. Cycle 4: After refmac, R = 0.2395 (Rfree = 0.000) for 5924 atoms. Found 26 (66 requested) and removed 37 (35 requested) atoms. Cycle 5: After refmac, R = 0.2339 (Rfree = 0.000) for 5896 atoms. Found 32 (64 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.43 2.53 Search for helices and strands: 0 residues in 0 chains, 6062 seeds are put forward NCS extension: 48 residues added (26 deleted due to clashes), 6110 seeds are put forward Round 1: 553 peptides, 65 chains. Longest chain 23 peptides. Score 0.676 Round 2: 616 peptides, 52 chains. Longest chain 34 peptides. Score 0.794 Round 3: 619 peptides, 53 chains. Longest chain 42 peptides. Score 0.793 Round 4: 611 peptides, 46 chains. Longest chain 43 peptides. Score 0.813 Round 5: 623 peptides, 50 chains. Longest chain 40 peptides. Score 0.807 Taking the results from Round 4 Chains 58, Residues 565, Estimated correctness of the model 89.3 % 16 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 193 A and 201 A Built loop between residues 277 A and 282 A 55 chains (572 residues) following loop building 14 chains (296 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9843 restraints for refining 6070 atoms. 6487 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2722 (Rfree = 0.000) for 6070 atoms. Found 65 (65 requested) and removed 74 (36 requested) atoms. Cycle 7: After refmac, R = 0.2513 (Rfree = 0.000) for 6014 atoms. Found 46 (63 requested) and removed 41 (36 requested) atoms. Cycle 8: After refmac, R = 0.2401 (Rfree = 0.000) for 5991 atoms. Found 47 (61 requested) and removed 37 (35 requested) atoms. Cycle 9: After refmac, R = 0.2310 (Rfree = 0.000) for 5982 atoms. Found 28 (60 requested) and removed 36 (35 requested) atoms. Cycle 10: After refmac, R = 0.2250 (Rfree = 0.000) for 5953 atoms. Found 32 (57 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.42 2.52 Search for helices and strands: 0 residues in 0 chains, 6083 seeds are put forward NCS extension: 83 residues added (6 deleted due to clashes), 6166 seeds are put forward Round 1: 568 peptides, 52 chains. Longest chain 35 peptides. Score 0.754 Round 2: 609 peptides, 45 chains. Longest chain 51 peptides. Score 0.815 Round 3: 620 peptides, 48 chains. Longest chain 54 peptides. Score 0.812 Round 4: 629 peptides, 42 chains. Longest chain 54 peptides. Score 0.838 Round 5: 612 peptides, 53 chains. Longest chain 41 peptides. Score 0.788 Taking the results from Round 4 Chains 45, Residues 587, Estimated correctness of the model 91.7 % 14 chains (317 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 193 A and 200 A Built loop between residues 269 A and 273 A Built loop between residues 35 B and 46 B 40 chains (600 residues) following loop building 11 chains (336 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9182 restraints for refining 6070 atoms. 5513 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2639 (Rfree = 0.000) for 6070 atoms. Found 58 (58 requested) and removed 71 (36 requested) atoms. Cycle 12: After refmac, R = 0.2468 (Rfree = 0.000) for 6013 atoms. Found 52 (55 requested) and removed 38 (35 requested) atoms. Cycle 13: After refmac, R = 0.2383 (Rfree = 0.000) for 6002 atoms. Found 38 (54 requested) and removed 35 (35 requested) atoms. Cycle 14: After refmac, R = 0.2298 (Rfree = 0.000) for 5988 atoms. Found 27 (53 requested) and removed 35 (35 requested) atoms. Cycle 15: After refmac, R = 0.2261 (Rfree = 0.000) for 5965 atoms. Found 26 (51 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.45 2.55 Search for helices and strands: 0 residues in 0 chains, 6090 seeds are put forward NCS extension: 24 residues added (58 deleted due to clashes), 6114 seeds are put forward Round 1: 601 peptides, 46 chains. Longest chain 47 peptides. Score 0.806 Round 2: 634 peptides, 39 chains. Longest chain 54 peptides. Score 0.851 Round 3: 615 peptides, 46 chains. Longest chain 41 peptides. Score 0.816 Round 4: 642 peptides, 42 chains. Longest chain 56 peptides. Score 0.846 Round 5: 627 peptides, 46 chains. Longest chain 47 peptides. Score 0.824 Taking the results from Round 2 Chains 40, Residues 595, Estimated correctness of the model 92.9 % 15 chains (412 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 191 A and 195 A Built loop between residues 241 A and 244 A Built loop between residues 257 A and 261 A Built loop between residues 277 A and 280 A Built loop between residues 222 B and 226 B 36 chains (604 residues) following loop building 10 chains (425 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8352 restraints for refining 6069 atoms. 4312 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2607 (Rfree = 0.000) for 6069 atoms. Found 50 (50 requested) and removed 81 (36 requested) atoms. Cycle 17: After refmac, R = 0.2426 (Rfree = 0.000) for 5996 atoms. Found 48 (48 requested) and removed 36 (35 requested) atoms. Cycle 18: After refmac, R = 0.2309 (Rfree = 0.000) for 5992 atoms. Found 37 (47 requested) and removed 35 (35 requested) atoms. Cycle 19: After refmac, R = 0.2245 (Rfree = 0.000) for 5980 atoms. Found 22 (45 requested) and removed 35 (35 requested) atoms. Cycle 20: After refmac, R = 0.2193 (Rfree = 0.000) for 5955 atoms. Found 29 (43 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.45 2.55 Search for helices and strands: 0 residues in 0 chains, 6098 seeds are put forward NCS extension: 23 residues added (76 deleted due to clashes), 6121 seeds are put forward Round 1: 580 peptides, 43 chains. Longest chain 55 peptides. Score 0.801 Round 2: 603 peptides, 45 chains. Longest chain 56 peptides. Score 0.811 Round 3: 612 peptides, 49 chains. Longest chain 54 peptides. Score 0.803 Round 4: 625 peptides, 46 chains. Longest chain 45 peptides. Score 0.822 Round 5: 623 peptides, 47 chains. Longest chain 51 peptides. Score 0.818 Taking the results from Round 4 Chains 52, Residues 579, Estimated correctness of the model 90.2 % 16 chains (341 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 218 A and 221 A Built loop between residues 255 B and 261 B 49 chains (582 residues) following loop building 14 chains (348 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9183 restraints for refining 6070 atoms. 5559 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2542 (Rfree = 0.000) for 6070 atoms. Found 43 (43 requested) and removed 63 (36 requested) atoms. Cycle 22: After refmac, R = 0.2364 (Rfree = 0.000) for 6026 atoms. Found 41 (41 requested) and removed 36 (35 requested) atoms. Cycle 23: After refmac, R = 0.2255 (Rfree = 0.000) for 6015 atoms. Found 28 (40 requested) and removed 36 (35 requested) atoms. Cycle 24: After refmac, R = 0.2209 (Rfree = 0.000) for 5992 atoms. Found 23 (38 requested) and removed 36 (35 requested) atoms. Cycle 25: After refmac, R = 0.2151 (Rfree = 0.000) for 5962 atoms. Found 25 (37 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.44 2.54 Search for helices and strands: 0 residues in 0 chains, 6067 seeds are put forward NCS extension: 24 residues added (25 deleted due to clashes), 6091 seeds are put forward Round 1: 594 peptides, 49 chains. Longest chain 37 peptides. Score 0.789 Round 2: 625 peptides, 44 chains. Longest chain 44 peptides. Score 0.829 Round 3: 614 peptides, 48 chains. Longest chain 40 peptides. Score 0.808 Round 4: 609 peptides, 48 chains. Longest chain 39 peptides. Score 0.804 Round 5: 610 peptides, 45 chains. Longest chain 39 peptides. Score 0.816 Taking the results from Round 2 Chains 52, Residues 581, Estimated correctness of the model 90.9 % 18 chains (370 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 230 A and 237 A Built loop between residues 258 A and 261 A Built loop between residues 363 B and 366 B 48 chains (588 residues) following loop building 15 chains (380 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8687 restraints for refining 6070 atoms. 4874 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2497 (Rfree = 0.000) for 6070 atoms. Found 36 (36 requested) and removed 70 (36 requested) atoms. Cycle 27: After refmac, R = 0.2337 (Rfree = 0.000) for 6011 atoms. Found 35 (35 requested) and removed 36 (35 requested) atoms. Cycle 28: After refmac, R = 0.2258 (Rfree = 0.000) for 5996 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 29: After refmac, R = 0.2209 (Rfree = 0.000) for 5981 atoms. Found 24 (35 requested) and removed 35 (35 requested) atoms. Cycle 30: After refmac, R = 0.2169 (Rfree = 0.000) for 5958 atoms. Found 21 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.45 2.55 Search for helices and strands: 0 residues in 0 chains, 6111 seeds are put forward NCS extension: 22 residues added (23 deleted due to clashes), 6133 seeds are put forward Round 1: 572 peptides, 50 chains. Longest chain 38 peptides. Score 0.766 Round 2: 616 peptides, 43 chains. Longest chain 43 peptides. Score 0.827 Round 3: 624 peptides, 44 chains. Longest chain 40 peptides. Score 0.829 Round 4: 614 peptides, 47 chains. Longest chain 43 peptides. Score 0.811 Round 5: 636 peptides, 43 chains. Longest chain 45 peptides. Score 0.839 Taking the results from Round 5 Chains 47, Residues 593, Estimated correctness of the model 91.8 % 18 chains (407 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 264 A and 269 A Built loop between residues 287 A and 290 A Built loop between residues 222 B and 232 B 41 chains (602 residues) following loop building 15 chains (422 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8431 restraints for refining 6070 atoms. 4486 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2601 (Rfree = 0.000) for 6070 atoms. Found 36 (36 requested) and removed 60 (36 requested) atoms. Cycle 32: After refmac, R = 0.2398 (Rfree = 0.000) for 6028 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 33: After refmac, R = 0.2296 (Rfree = 0.000) for 5997 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 34: After refmac, R = 0.2209 (Rfree = 0.000) for 5989 atoms. Found 26 (35 requested) and removed 35 (35 requested) atoms. Cycle 35: After refmac, R = 0.2134 (Rfree = 0.000) for 5967 atoms. Found 29 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.44 2.54 Search for helices and strands: 0 residues in 0 chains, 6107 seeds are put forward NCS extension: 34 residues added (44 deleted due to clashes), 6141 seeds are put forward Round 1: 589 peptides, 47 chains. Longest chain 43 peptides. Score 0.793 Round 2: 623 peptides, 42 chains. Longest chain 50 peptides. Score 0.835 Round 3: 609 peptides, 45 chains. Longest chain 43 peptides. Score 0.815 Round 4: 621 peptides, 39 chains. Longest chain 43 peptides. Score 0.843 Round 5: 607 peptides, 41 chains. Longest chain 51 peptides. Score 0.828 Taking the results from Round 4 Chains 46, Residues 582, Estimated correctness of the model 92.2 % 18 chains (420 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 242 B and 245 B Built loop between residues 308 B and 314 B Built loop between residues 382 B and 386 B 42 chains (591 residues) following loop building 15 chains (430 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8245 restraints for refining 6069 atoms. 4230 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2500 (Rfree = 0.000) for 6069 atoms. Found 36 (36 requested) and removed 76 (36 requested) atoms. Cycle 37: After refmac, R = 0.2343 (Rfree = 0.000) for 5997 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 38: After refmac, R = 0.2247 (Rfree = 0.000) for 5978 atoms. Found 30 (35 requested) and removed 37 (35 requested) atoms. Cycle 39: After refmac, R = 0.2172 (Rfree = 0.000) for 5963 atoms. Found 30 (35 requested) and removed 35 (35 requested) atoms. Cycle 40: After refmac, R = 0.2104 (Rfree = 0.000) for 5953 atoms. Found 23 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.45 2.55 Search for helices and strands: 0 residues in 0 chains, 6094 seeds are put forward NCS extension: 19 residues added (29 deleted due to clashes), 6113 seeds are put forward Round 1: 575 peptides, 44 chains. Longest chain 42 peptides. Score 0.794 Round 2: 610 peptides, 43 chains. Longest chain 45 peptides. Score 0.823 Round 3: 590 peptides, 49 chains. Longest chain 47 peptides. Score 0.786 Round 4: 589 peptides, 49 chains. Longest chain 42 peptides. Score 0.785 Round 5: 600 peptides, 44 chains. Longest chain 47 peptides. Score 0.812 Taking the results from Round 2 Chains 51, Residues 567, Estimated correctness of the model 90.3 % 18 chains (362 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 41 A Built loop between residues 48 A and 54 A 49 chains (574 residues) following loop building 16 chains (372 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8871 restraints for refining 6069 atoms. 5177 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2522 (Rfree = 0.000) for 6069 atoms. Found 36 (36 requested) and removed 77 (36 requested) atoms. Cycle 42: After refmac, R = 0.2330 (Rfree = 0.000) for 6015 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 43: After refmac, R = 0.2238 (Rfree = 0.000) for 5996 atoms. Found 30 (35 requested) and removed 35 (35 requested) atoms. Cycle 44: After refmac, R = 0.2172 (Rfree = 0.000) for 5977 atoms. Found 33 (35 requested) and removed 35 (35 requested) atoms. Cycle 45: After refmac, R = 0.2124 (Rfree = 0.000) for 5962 atoms. Found 24 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.54 Search for helices and strands: 0 residues in 0 chains, 6093 seeds are put forward NCS extension: 25 residues added (36 deleted due to clashes), 6118 seeds are put forward Round 1: 581 peptides, 41 chains. Longest chain 49 peptides. Score 0.810 Round 2: 594 peptides, 43 chains. Longest chain 43 peptides. Score 0.812 Round 3: 600 peptides, 44 chains. Longest chain 35 peptides. Score 0.812 Round 4: 600 peptides, 48 chains. Longest chain 54 peptides. Score 0.797 Round 5: 594 peptides, 42 chains. Longest chain 43 peptides. Score 0.815 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 552, Estimated correctness of the model 89.5 % 15 chains (326 residues) have been docked in sequence Sequence coverage is 58 % Consider running further cycles of model building using 1vkz-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 33 A and 46 A Built loop between residues 363 B and 369 B 42 chains (563 residues) following loop building 13 chains (343 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17874 reflections ( 95.70 % complete ) and 9186 restraints for refining 6070 atoms. 5624 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2435 (Rfree = 0.000) for 6070 atoms. Found 0 (36 requested) and removed 13 (36 requested) atoms. Cycle 47: After refmac, R = 0.2290 (Rfree = 0.000) for 6039 atoms. Found 0 (35 requested) and removed 6 (35 requested) atoms. Cycle 48: After refmac, R = 0.2229 (Rfree = 0.000) for 6028 atoms. Found 0 (35 requested) and removed 9 (35 requested) atoms. Cycle 49: After refmac, R = 0.2180 (Rfree = 0.000) for 6016 atoms. Found 0 (35 requested) and removed 10 (35 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:05:21 GMT 2018 Job finished. TimeTaking 97.39 Used memory is bytes: 10752912