Mon 24 Dec 08:05:36 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 2ii1-1.9-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-1.9-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-1.9-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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/2ii1-1.9-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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 08:05:41 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/2ii1-1.9-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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 1083 and 0 Target number of residues in the AU: 1083 Target solvent content: 0.4721 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-1.9-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-1.9-parrot-noncs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.45 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: 91.283 1.950 Wilson plot Bfac: 18.16 70806 reflections ( 90.30 % complete ) and 0 restraints for refining 10707 atoms. Observations/parameters ratio is 1.65 ------------------------------------------------------ Starting model: R = 0.3398 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2910 (Rfree = 0.000) for 10707 atoms. Found 220 (394 requested) and removed 213 (197 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.95 2.20 NCS extension: 0 residues added, 10714 seeds are put forward Round 1: 509 peptides, 101 chains. Longest chain 11 peptides. Score 0.335 Round 2: 537 peptides, 94 chains. Longest chain 14 peptides. Score 0.418 Round 3: 575 peptides, 83 chains. Longest chain 25 peptides. Score 0.529 Round 4: 639 peptides, 83 chains. Longest chain 24 peptides. Score 0.602 Round 5: 623 peptides, 69 chains. Longest chain 50 peptides. Score 0.650 Taking the results from Round 5 Chains 79, Residues 554, Estimated correctness of the model 90.4 % 13 chains (163 residues) have been docked in sequence ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 18526 restraints for refining 9379 atoms. 15912 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3193 (Rfree = 0.000) for 9379 atoms. Found 280 (345 requested) and removed 183 (172 requested) atoms. Cycle 2: After refmac, R = 0.2974 (Rfree = 0.000) for 9457 atoms. Found 147 (348 requested) and removed 119 (174 requested) atoms. Cycle 3: After refmac, R = 0.2800 (Rfree = 0.000) for 9453 atoms. Found 138 (349 requested) and removed 36 (174 requested) atoms. Cycle 4: After refmac, R = 0.2675 (Rfree = 0.000) for 9537 atoms. Found 135 (351 requested) and removed 33 (175 requested) atoms. Cycle 5: After refmac, R = 0.2593 (Rfree = 0.000) for 9620 atoms. Found 82 (354 requested) and removed 23 (177 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.92 2.17 NCS extension: 10 residues added (5 deleted due to clashes), 9736 seeds are put forward Round 1: 619 peptides, 79 chains. Longest chain 28 peptides. Score 0.600 Round 2: 634 peptides, 68 chains. Longest chain 54 peptides. Score 0.665 Round 3: 650 peptides, 69 chains. Longest chain 31 peptides. Score 0.675 Round 4: 647 peptides, 66 chains. Longest chain 32 peptides. Score 0.685 Round 5: 665 peptides, 66 chains. Longest chain 32 peptides. Score 0.701 Taking the results from Round 5 Chains 74, Residues 599, Estimated correctness of the model 92.8 % 14 chains (163 residues) have been docked in sequence Building loops using Loopy2018 74 chains (599 residues) following loop building 14 chains (163 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 18317 restraints for refining 9389 atoms. 15518 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2826 (Rfree = 0.000) for 9389 atoms. Found 256 (345 requested) and removed 146 (172 requested) atoms. Cycle 7: After refmac, R = 0.2640 (Rfree = 0.000) for 9489 atoms. Found 146 (342 requested) and removed 29 (174 requested) atoms. Cycle 8: After refmac, R = 0.2526 (Rfree = 0.000) for 9596 atoms. Found 106 (346 requested) and removed 26 (176 requested) atoms. Cycle 9: After refmac, R = 0.2451 (Rfree = 0.000) for 9669 atoms. Found 113 (349 requested) and removed 23 (178 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2390 (Rfree = 0.000) for 9754 atoms. Found 76 (352 requested) and removed 19 (179 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.90 2.14 NCS extension: 5 residues added (12 deleted due to clashes), 9861 seeds are put forward Round 1: 654 peptides, 71 chains. Longest chain 30 peptides. Score 0.671 Round 2: 657 peptides, 59 chains. Longest chain 32 peptides. Score 0.722 Round 3: 677 peptides, 64 chains. Longest chain 35 peptides. Score 0.719 Round 4: 675 peptides, 62 chains. Longest chain 32 peptides. Score 0.725 Round 5: 658 peptides, 66 chains. Longest chain 49 peptides. Score 0.695 Taking the results from Round 4 Chains 72, Residues 613, Estimated correctness of the model 93.9 % 15 chains (183 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 269 C and 278 C 69 chains (619 residues) following loop building 14 chains (191 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 18598 restraints for refining 9675 atoms. 15582 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2625 (Rfree = 0.000) for 9675 atoms. Found 236 (349 requested) and removed 136 (178 requested) atoms. Cycle 12: After refmac, R = 0.2476 (Rfree = 0.000) for 9764 atoms. Found 166 (345 requested) and removed 41 (179 requested) atoms. Cycle 13: After refmac, R = 0.2374 (Rfree = 0.000) for 9879 atoms. Found 133 (349 requested) and removed 31 (182 requested) atoms. Cycle 14: After refmac, R = 0.2305 (Rfree = 0.000) for 9974 atoms. Found 127 (352 requested) and removed 13 (183 requested) atoms. Cycle 15: After refmac, R = 0.2241 (Rfree = 0.000) for 10082 atoms. Found 89 (356 requested) and removed 23 (185 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.89 2.13 NCS extension: 9 residues added (6 deleted due to clashes), 10180 seeds are put forward Round 1: 644 peptides, 70 chains. Longest chain 35 peptides. Score 0.666 Round 2: 666 peptides, 59 chains. Longest chain 50 peptides. Score 0.729 Round 3: 667 peptides, 65 chains. Longest chain 49 peptides. Score 0.707 Round 4: 671 peptides, 63 chains. Longest chain 51 peptides. Score 0.718 Round 5: 663 peptides, 58 chains. Longest chain 49 peptides. Score 0.730 Taking the results from Round 5 Chains 67, Residues 605, Estimated correctness of the model 94.1 % 11 chains (183 residues) have been docked in sequence Building loops using Loopy2018 67 chains (605 residues) following loop building 11 chains (183 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 19162 restraints for refining 9859 atoms. 16225 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2503 (Rfree = 0.000) for 9859 atoms. Found 306 (348 requested) and removed 107 (181 requested) atoms. Cycle 17: After refmac, R = 0.2345 (Rfree = 0.000) for 10056 atoms. Found 167 (355 requested) and removed 38 (185 requested) atoms. Cycle 18: After refmac, R = 0.2248 (Rfree = 0.000) for 10179 atoms. Found 137 (360 requested) and removed 22 (187 requested) atoms. Cycle 19: After refmac, R = 0.2168 (Rfree = 0.000) for 10287 atoms. Found 106 (364 requested) and removed 22 (189 requested) atoms. Cycle 20: After refmac, R = 0.2118 (Rfree = 0.000) for 10366 atoms. Found 109 (366 requested) and removed 26 (190 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.88 2.12 NCS extension: 13 residues added (19 deleted due to clashes), 10476 seeds are put forward Round 1: 648 peptides, 66 chains. Longest chain 33 peptides. Score 0.686 Round 2: 662 peptides, 59 chains. Longest chain 33 peptides. Score 0.726 Round 3: 674 peptides, 58 chains. Longest chain 45 peptides. Score 0.739 Round 4: 653 peptides, 58 chains. Longest chain 50 peptides. Score 0.722 Round 5: 682 peptides, 60 chains. Longest chain 34 peptides. Score 0.737 Taking the results from Round 3 Chains 67, Residues 616, Estimated correctness of the model 94.4 % 13 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 120 D and 130 D 66 chains (624 residues) following loop building 12 chains (210 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 19439 restraints for refining 10153 atoms. 16363 conditional restraints added. Observations/parameters ratio is 1.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2411 (Rfree = 0.000) for 10153 atoms. Found 293 (358 requested) and removed 137 (186 requested) atoms. Cycle 22: After refmac, R = 0.2251 (Rfree = 0.000) for 10306 atoms. Found 201 (364 requested) and removed 37 (189 requested) atoms. Cycle 23: After refmac, R = 0.2167 (Rfree = 0.000) for 10463 atoms. Found 147 (370 requested) and removed 27 (192 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2101 (Rfree = 0.000) for 10577 atoms. Found 119 (373 requested) and removed 36 (194 requested) atoms. Cycle 25: After refmac, R = 0.2056 (Rfree = 0.000) for 10652 atoms. Found 115 (376 requested) and removed 25 (196 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.89 2.13 NCS extension: 10 residues added (16 deleted due to clashes), 10783 seeds are put forward Round 1: 661 peptides, 66 chains. Longest chain 33 peptides. Score 0.698 Round 2: 684 peptides, 57 chains. Longest chain 51 peptides. Score 0.750 Round 3: 666 peptides, 65 chains. Longest chain 42 peptides. Score 0.706 Round 4: 668 peptides, 57 chains. Longest chain 49 peptides. Score 0.738 Round 5: 666 peptides, 59 chains. Longest chain 49 peptides. Score 0.729 Taking the results from Round 2 Chains 61, Residues 627, Estimated correctness of the model 94.8 % 14 chains (271 residues) have been docked in sequence Building loops using Loopy2018 61 chains (627 residues) following loop building 14 chains (271 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 19726 restraints for refining 10548 atoms. 16357 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2299 (Rfree = 0.000) for 10548 atoms. Found 349 (372 requested) and removed 148 (194 requested) atoms. Cycle 27: After refmac, R = 0.2171 (Rfree = 0.000) for 10743 atoms. Found 174 (379 requested) and removed 41 (197 requested) atoms. Cycle 28: After refmac, R = 0.2087 (Rfree = 0.000) for 10868 atoms. Found 144 (384 requested) and removed 30 (200 requested) atoms. Cycle 29: After refmac, R = 0.2034 (Rfree = 0.000) for 10973 atoms. Found 137 (388 requested) and removed 44 (202 requested) atoms. Cycle 30: After refmac, R = 0.2006 (Rfree = 0.000) for 11059 atoms. Found 127 (391 requested) and removed 32 (203 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.88 2.12 NCS extension: 19 residues added (16 deleted due to clashes), 11188 seeds are put forward Round 1: 650 peptides, 63 chains. Longest chain 36 peptides. Score 0.700 Round 2: 662 peptides, 61 chains. Longest chain 46 peptides. Score 0.718 Round 3: 657 peptides, 60 chains. Longest chain 36 peptides. Score 0.718 Round 4: 686 peptides, 67 chains. Longest chain 44 peptides. Score 0.714 Round 5: 666 peptides, 63 chains. Longest chain 51 peptides. Score 0.714 Taking the results from Round 3 Chains 70, Residues 597, Estimated correctness of the model 93.6 % 12 chains (192 residues) have been docked in sequence Building loops using Loopy2018 70 chains (597 residues) following loop building 12 chains (192 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 70806 reflections ( 90.30 % complete ) and 21101 restraints for refining 10735 atoms. 18155 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2217 (Rfree = 0.000) for 10735 atoms. Found 348 (379 requested) and removed 110 (197 requested) atoms. Cycle 32: After refmac, R = 0.2074 (Rfree = 0.000) for 10970 atoms. Found 231 (388 requested) and removed 38 (202 requested) atoms. Cycle 33: After refmac, R = 0.1989 (Rfree = 0.000) for 11157 atoms. Found 183 (395 requested) and removed 54 (205 requested) atoms. Cycle 34: After refmac, R = 0.1938 (Rfree = 0.000) for 11282 atoms. Found 159 (398 requested) and removed 51 (207 requested) atoms. Cycle 35: After refmac, R = 0.1890 (Rfree = 0.000) for 11386 atoms. Found 151 (402 requested) and removed 59 (209 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.87 2.11 NCS extension: 13 residues added (20 deleted due to clashes), 11504 seeds are put forward Round 1: 635 peptides, 64 chains. Longest chain 32 peptides. Score 0.683 Round 2: 659 peptides, 56 chains. Longest chain 51 peptides. Score 0.735 Round 3: 664 peptides, 60 chains. Longest chain 43 peptides. Score 0.724 Round 4: 665 peptides, 60 chains. Longest chain 51 peptides. Score 0.724 Round 5: 655 peptides, 63 chains. Longest chain 33 peptides. Score 0.704 Taking the results from Round 2 Chains 61, Residues 603, Estimated correctness of the model 94.3 % 10 chains (136 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 140 A and 143 A 60 chains (605 residues) following loop building 9 chains (138 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 22233 restraints for refining 10949 atoms. 19435 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2093 (Rfree = 0.000) for 10949 atoms. Found 372 (387 requested) and removed 74 (201 requested) atoms. Cycle 37: After refmac, R = 0.1971 (Rfree = 0.000) for 11244 atoms. Found 243 (397 requested) and removed 53 (207 requested) atoms. Cycle 38: After refmac, R = 0.1886 (Rfree = 0.000) for 11429 atoms. Found 180 (404 requested) and removed 51 (210 requested) atoms. Cycle 39: After refmac, R = 0.1852 (Rfree = 0.000) for 11553 atoms. Found 197 (408 requested) and removed 74 (212 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1814 (Rfree = 0.000) for 11671 atoms. Found 181 (412 requested) and removed 83 (214 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.88 2.12 NCS extension: 24 residues added (21 deleted due to clashes), 11799 seeds are put forward Round 1: 639 peptides, 66 chains. Longest chain 32 peptides. Score 0.678 Round 2: 664 peptides, 58 chains. Longest chain 51 peptides. Score 0.731 Round 3: 655 peptides, 64 chains. Longest chain 41 peptides. Score 0.700 Round 4: 660 peptides, 57 chains. Longest chain 50 peptides. Score 0.732 Round 5: 648 peptides, 61 chains. Longest chain 41 peptides. Score 0.707 Taking the results from Round 4 Chains 62, Residues 603, Estimated correctness of the model 94.1 % 8 chains (156 residues) have been docked in sequence Building loops using Loopy2018 62 chains (603 residues) following loop building 8 chains (156 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 70806 reflections ( 90.30 % complete ) and 22536 restraints for refining 11155 atoms. 19669 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2098 (Rfree = 0.000) for 11155 atoms. Found 394 (394 requested) and removed 102 (205 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1941 (Rfree = 0.000) for 11444 atoms. Found 240 (404 requested) and removed 51 (210 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1862 (Rfree = 0.000) for 11628 atoms. Found 182 (411 requested) and removed 69 (214 requested) atoms. Cycle 44: After refmac, R = 0.1815 (Rfree = 0.000) for 11731 atoms. Found 180 (415 requested) and removed 78 (216 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1778 (Rfree = 0.000) for 11826 atoms. Found 168 (418 requested) and removed 88 (217 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.88 2.12 NCS extension: 8 residues added (13 deleted due to clashes), 11924 seeds are put forward Round 1: 628 peptides, 64 chains. Longest chain 30 peptides. Score 0.677 Round 2: 639 peptides, 57 chains. Longest chain 45 peptides. Score 0.715 Round 3: 628 peptides, 59 chains. Longest chain 43 peptides. Score 0.698 Round 4: 650 peptides, 58 chains. Longest chain 54 peptides. Score 0.720 Round 5: 639 peptides, 59 chains. Longest chain 50 peptides. Score 0.707 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 592, Estimated correctness of the model 93.6 % 12 chains (167 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2ii1-1_warpNtrace.pdb as input Building loops using Loopy2018 67 chains (592 residues) following loop building 12 chains (167 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 70806 reflections ( 90.30 % complete ) and 22774 restraints for refining 11305 atoms. 19931 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2066 (Rfree = 0.000) for 11305 atoms. Found 0 (391 requested) and removed 23 (208 requested) atoms. Cycle 47: After refmac, R = 0.1983 (Rfree = 0.000) for 11279 atoms. Found 0 (382 requested) and removed 5 (207 requested) atoms. Cycle 48: After refmac, R = 0.1943 (Rfree = 0.000) for 11272 atoms. Found 0 (373 requested) and removed 4 (207 requested) atoms. Cycle 49: After refmac, R = 0.1920 (Rfree = 0.000) for 11267 atoms. TimeTaking 116.37