Mon 24 Dec 07:36:09 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 2prr-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prr-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-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/2prr-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-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 07:36:14 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/2prr-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-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 1940 and 0 Target number of residues in the AU: 1940 Target solvent content: 0.6319 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-3.2-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.80 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. 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: 119.307 3.200 Wilson plot Bfac: 67.47 44474 reflections ( 97.55 % complete ) and 0 restraints for refining 21055 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3102 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2375 (Rfree = 0.000) for 21055 atoms. Found 113 (188 requested) and removed 199 (94 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 21589 seeds are put forward NCS extension: 0 residues added, 21589 seeds are put forward Round 1: 1201 peptides, 219 chains. Longest chain 18 peptides. Score 0.372 Round 2: 1393 peptides, 209 chains. Longest chain 24 peptides. Score 0.498 Round 3: 1418 peptides, 193 chains. Longest chain 25 peptides. Score 0.544 Round 4: 1460 peptides, 200 chains. Longest chain 27 peptides. Score 0.549 Round 5: 1458 peptides, 192 chains. Longest chain 22 peptides. Score 0.564 Taking the results from Round 5 Chains 198, Residues 1266, Estimated correctness of the model 31.0 % 13 chains (132 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5385 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2124 (Rfree = 0.000) for 17266 atoms. Found 89 (154 requested) and removed 109 (77 requested) atoms. Cycle 2: After refmac, R = 0.1967 (Rfree = 0.000) for 17246 atoms. Found 30 (154 requested) and removed 81 (77 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1877 (Rfree = 0.000) for 17195 atoms. Found 20 (154 requested) and removed 83 (77 requested) atoms. Cycle 4: After refmac, R = 0.1828 (Rfree = 0.000) for 17132 atoms. Found 25 (153 requested) and removed 78 (76 requested) atoms. Cycle 5: After refmac, R = 0.1756 (Rfree = 0.000) for 17079 atoms. Found 10 (153 requested) and removed 81 (76 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17739 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 17755 seeds are put forward Round 1: 1315 peptides, 208 chains. Longest chain 26 peptides. Score 0.460 Round 2: 1463 peptides, 187 chains. Longest chain 30 peptides. Score 0.576 Round 3: 1454 peptides, 188 chains. Longest chain 27 peptides. Score 0.570 Round 4: 1457 peptides, 182 chains. Longest chain 29 peptides. Score 0.584 Round 5: 1466 peptides, 179 chains. Longest chain 33 peptides. Score 0.593 Taking the results from Round 5 Chains 182, Residues 1287, Estimated correctness of the model 39.2 % 11 chains (105 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5372 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2001 (Rfree = 0.000) for 17266 atoms. Found 98 (154 requested) and removed 96 (77 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1841 (Rfree = 0.000) for 17268 atoms. Found 33 (154 requested) and removed 82 (77 requested) atoms. Cycle 8: After refmac, R = 0.1766 (Rfree = 0.000) for 17219 atoms. Found 20 (154 requested) and removed 80 (77 requested) atoms. Cycle 9: After refmac, R = 0.1735 (Rfree = 0.000) for 17159 atoms. Found 17 (153 requested) and removed 81 (76 requested) atoms. Cycle 10: After refmac, R = 0.1694 (Rfree = 0.000) for 17095 atoms. Found 14 (153 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17704 seeds are put forward NCS extension: 34 residues added (6 deleted due to clashes), 17738 seeds are put forward Round 1: 1288 peptides, 200 chains. Longest chain 25 peptides. Score 0.465 Round 2: 1425 peptides, 186 chains. Longest chain 27 peptides. Score 0.561 Round 3: 1436 peptides, 183 chains. Longest chain 24 peptides. Score 0.572 Round 4: 1434 peptides, 185 chains. Longest chain 21 peptides. Score 0.567 Round 5: 1459 peptides, 190 chains. Longest chain 26 peptides. Score 0.569 Taking the results from Round 3 Chains 189, Residues 1253, Estimated correctness of the model 33.3 % 10 chains (92 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5202 restraints for refining 17263 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1935 (Rfree = 0.000) for 17263 atoms. Found 100 (154 requested) and removed 103 (77 requested) atoms. Cycle 12: After refmac, R = 0.1806 (Rfree = 0.000) for 17260 atoms. Found 18 (154 requested) and removed 79 (77 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1786 (Rfree = 0.000) for 17199 atoms. Found 18 (154 requested) and removed 80 (77 requested) atoms. Cycle 14: After refmac, R = 0.1742 (Rfree = 0.000) for 17137 atoms. Found 16 (153 requested) and removed 78 (76 requested) atoms. Cycle 15: After refmac, R = 0.1734 (Rfree = 0.000) for 17075 atoms. Found 20 (153 requested) and removed 80 (76 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17677 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 17699 seeds are put forward Round 1: 1284 peptides, 204 chains. Longest chain 20 peptides. Score 0.453 Round 2: 1420 peptides, 187 chains. Longest chain 21 peptides. Score 0.557 Round 3: 1427 peptides, 182 chains. Longest chain 23 peptides. Score 0.570 Round 4: 1427 peptides, 194 chains. Longest chain 22 peptides. Score 0.546 Round 5: 1407 peptides, 186 chains. Longest chain 30 peptides. Score 0.553 Taking the results from Round 3 Chains 189, Residues 1245, Estimated correctness of the model 32.7 % 13 chains (119 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5239 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1892 (Rfree = 0.000) for 17266 atoms. Found 96 (154 requested) and removed 104 (77 requested) atoms. Cycle 17: After refmac, R = 0.1765 (Rfree = 0.000) for 17258 atoms. Found 24 (154 requested) and removed 84 (77 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1745 (Rfree = 0.000) for 17198 atoms. Found 24 (154 requested) and removed 77 (77 requested) atoms. Cycle 19: After refmac, R = 0.1728 (Rfree = 0.000) for 17145 atoms. Found 19 (153 requested) and removed 77 (76 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1675 (Rfree = 0.000) for 17087 atoms. Found 16 (153 requested) and removed 76 (76 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17686 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 17702 seeds are put forward Round 1: 1231 peptides, 200 chains. Longest chain 21 peptides. Score 0.434 Round 2: 1376 peptides, 194 chains. Longest chain 22 peptides. Score 0.522 Round 3: 1342 peptides, 192 chains. Longest chain 18 peptides. Score 0.510 Round 4: 1366 peptides, 187 chains. Longest chain 23 peptides. Score 0.532 Round 5: 1352 peptides, 187 chains. Longest chain 22 peptides. Score 0.525 Taking the results from Round 4 Chains 191, Residues 1179, Estimated correctness of the model 21.4 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4714 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1854 (Rfree = 0.000) for 17266 atoms. Found 71 (154 requested) and removed 90 (77 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1761 (Rfree = 0.000) for 17247 atoms. Found 37 (154 requested) and removed 81 (77 requested) atoms. Cycle 23: After refmac, R = 0.1704 (Rfree = 0.000) for 17203 atoms. Found 23 (154 requested) and removed 83 (77 requested) atoms. Cycle 24: After refmac, R = 0.1701 (Rfree = 0.000) for 17143 atoms. Found 27 (153 requested) and removed 78 (76 requested) atoms. Cycle 25: After refmac, R = 0.1663 (Rfree = 0.000) for 17092 atoms. Found 28 (153 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 17689 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 17707 seeds are put forward Round 1: 1210 peptides, 207 chains. Longest chain 18 peptides. Score 0.406 Round 2: 1332 peptides, 196 chains. Longest chain 20 peptides. Score 0.496 Round 3: 1359 peptides, 187 chains. Longest chain 20 peptides. Score 0.529 Round 4: 1353 peptides, 182 chains. Longest chain 24 peptides. Score 0.536 Round 5: 1361 peptides, 189 chains. Longest chain 20 peptides. Score 0.525 Taking the results from Round 4 Chains 185, Residues 1171, Estimated correctness of the model 22.7 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4653 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1799 (Rfree = 0.000) for 17266 atoms. Found 76 (154 requested) and removed 89 (77 requested) atoms. Cycle 27: After refmac, R = 0.1702 (Rfree = 0.000) for 17253 atoms. Found 31 (154 requested) and removed 77 (77 requested) atoms. Cycle 28: After refmac, R = 0.1649 (Rfree = 0.000) for 17207 atoms. Found 29 (154 requested) and removed 79 (77 requested) atoms. Cycle 29: After refmac, R = 0.1644 (Rfree = 0.000) for 17157 atoms. Found 24 (153 requested) and removed 78 (76 requested) atoms. Cycle 30: After refmac, R = 0.1600 (Rfree = 0.000) for 17103 atoms. Found 17 (153 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17680 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 17694 seeds are put forward Round 1: 1172 peptides, 201 chains. Longest chain 17 peptides. Score 0.399 Round 2: 1277 peptides, 177 chains. Longest chain 26 peptides. Score 0.511 Round 3: 1296 peptides, 187 chains. Longest chain 25 peptides. Score 0.498 Round 4: 1323 peptides, 184 chains. Longest chain 21 peptides. Score 0.518 Round 5: 1316 peptides, 188 chains. Longest chain 20 peptides. Score 0.506 Taking the results from Round 4 Chains 188, Residues 1139, Estimated correctness of the model 17.1 % 8 chains (75 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4686 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1788 (Rfree = 0.000) for 17266 atoms. Found 96 (154 requested) and removed 89 (77 requested) atoms. Cycle 32: After refmac, R = 0.1648 (Rfree = 0.000) for 17273 atoms. Found 22 (155 requested) and removed 78 (77 requested) atoms. Cycle 33: After refmac, R = 0.1621 (Rfree = 0.000) for 17217 atoms. Found 27 (154 requested) and removed 80 (77 requested) atoms. Cycle 34: After refmac, R = 0.1574 (Rfree = 0.000) for 17164 atoms. Found 28 (154 requested) and removed 77 (77 requested) atoms. Cycle 35: After refmac, R = 0.1547 (Rfree = 0.000) for 17115 atoms. Found 28 (153 requested) and removed 76 (76 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17712 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 17721 seeds are put forward Round 1: 1181 peptides, 209 chains. Longest chain 19 peptides. Score 0.385 Round 2: 1263 peptides, 186 chains. Longest chain 19 peptides. Score 0.483 Round 3: 1299 peptides, 199 chains. Longest chain 17 peptides. Score 0.473 Round 4: 1273 peptides, 186 chains. Longest chain 27 peptides. Score 0.489 Round 5: 1267 peptides, 189 chains. Longest chain 21 peptides. Score 0.479 Taking the results from Round 4 Chains 187, Residues 1087, Estimated correctness of the model 7.7 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4451 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1783 (Rfree = 0.000) for 17266 atoms. Found 67 (154 requested) and removed 96 (77 requested) atoms. Cycle 37: After refmac, R = 0.1661 (Rfree = 0.000) for 17237 atoms. Found 29 (154 requested) and removed 77 (77 requested) atoms. Cycle 38: After refmac, R = 0.1645 (Rfree = 0.000) for 17189 atoms. Found 28 (154 requested) and removed 79 (77 requested) atoms. Cycle 39: After refmac, R = 0.1594 (Rfree = 0.000) for 17138 atoms. Found 22 (153 requested) and removed 76 (76 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1567 (Rfree = 0.000) for 17084 atoms. Found 15 (153 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 17633 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 17651 seeds are put forward Round 1: 1093 peptides, 198 chains. Longest chain 15 peptides. Score 0.361 Round 2: 1215 peptides, 187 chains. Longest chain 19 peptides. Score 0.456 Round 3: 1253 peptides, 189 chains. Longest chain 19 peptides. Score 0.471 Round 4: 1218 peptides, 181 chains. Longest chain 20 peptides. Score 0.472 Round 5: 1207 peptides, 187 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 4 Chains 185, Residues 1037, Estimated correctness of the model 2.0 % 7 chains (68 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4201 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1743 (Rfree = 0.000) for 17266 atoms. Found 75 (154 requested) and removed 84 (77 requested) atoms. Cycle 42: After refmac, R = 0.1651 (Rfree = 0.000) for 17257 atoms. Found 32 (154 requested) and removed 78 (77 requested) atoms. Cycle 43: After refmac, R = 0.1607 (Rfree = 0.000) for 17211 atoms. Found 28 (154 requested) and removed 77 (77 requested) atoms. Cycle 44: After refmac, R = 0.1579 (Rfree = 0.000) for 17162 atoms. Found 12 (154 requested) and removed 78 (77 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1550 (Rfree = 0.000) for 17096 atoms. Found 19 (153 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17655 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 17669 seeds are put forward Round 1: 1020 peptides, 185 chains. Longest chain 14 peptides. Score 0.351 Round 2: 1195 peptides, 187 chains. Longest chain 17 peptides. Score 0.446 Round 3: 1167 peptides, 188 chains. Longest chain 16 peptides. Score 0.428 Round 4: 1148 peptides, 174 chains. Longest chain 18 peptides. Score 0.451 Round 5: 1174 peptides, 177 chains. Longest chain 21 peptides. Score 0.458 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 180, Residues 997, Estimated correctness of the model 0.0 % 5 chains (53 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 180 chains (997 residues) following loop building 5 chains (53 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 44474 reflections ( 97.55 % complete ) and 4013 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1718 (Rfree = 0.000) for 17266 atoms. Found 0 (154 requested) and removed 36 (77 requested) atoms. Cycle 47: After refmac, R = 0.1665 (Rfree = 0.000) for 17230 atoms. Found 0 (154 requested) and removed 26 (77 requested) atoms. Cycle 48: After refmac, R = 0.1640 (Rfree = 0.000) for 17204 atoms. Found 0 (154 requested) and removed 26 (77 requested) atoms. Cycle 49: After refmac, R = 0.1614 (Rfree = 0.000) for 17178 atoms. TimeTaking 156.78