Sun 23 Dec 22:22:49 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 2awa-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-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/2awa-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-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 ============================================================ Sun 23 Dec 22:22:58 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/2awa-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.8-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 1127 and 0 Target number of residues in the AU: 1127 Target solvent content: 0.6635 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-3.8-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: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.85 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: 135.654 3.800 Wilson plot Bfac: 87.31 17103 reflections ( 95.07 % complete ) and 0 restraints for refining 13842 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3541 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3159 (Rfree = 0.000) for 13842 atoms. Found 76 (76 requested) and removed 117 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 13965 seeds are put forward NCS extension: 0 residues added, 13965 seeds are put forward Round 1: 446 peptides, 97 chains. Longest chain 9 peptides. Score 0.234 Round 2: 559 peptides, 106 chains. Longest chain 17 peptides. Score 0.313 Round 3: 637 peptides, 113 chains. Longest chain 15 peptides. Score 0.359 Round 4: 654 peptides, 110 chains. Longest chain 14 peptides. Score 0.387 Round 5: 695 peptides, 120 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 4 Chains 110, Residues 544, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 27145 restraints for refining 11285 atoms. 25008 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2270 (Rfree = 0.000) for 11285 atoms. Found 41 (62 requested) and removed 67 (31 requested) atoms. Cycle 2: After refmac, R = 0.2169 (Rfree = 0.000) for 11113 atoms. Found 26 (61 requested) and removed 55 (30 requested) atoms. Cycle 3: After refmac, R = 0.2089 (Rfree = 0.000) for 11015 atoms. Found 33 (60 requested) and removed 64 (30 requested) atoms. Cycle 4: After refmac, R = 0.1697 (Rfree = 0.000) for 10945 atoms. Found 11 (60 requested) and removed 46 (30 requested) atoms. Cycle 5: After refmac, R = 0.1633 (Rfree = 0.000) for 10877 atoms. Found 6 (59 requested) and removed 44 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.51 Search for helices and strands: 0 residues in 0 chains, 11163 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 11181 seeds are put forward Round 1: 598 peptides, 121 chains. Longest chain 10 peptides. Score 0.288 Round 2: 697 peptides, 123 chains. Longest chain 13 peptides. Score 0.375 Round 3: 700 peptides, 113 chains. Longest chain 14 peptides. Score 0.416 Round 4: 723 peptides, 117 chains. Longest chain 16 peptides. Score 0.421 Round 5: 724 peptides, 116 chains. Longest chain 22 peptides. Score 0.426 Taking the results from Round 5 Chains 116, Residues 608, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26261 restraints for refining 11286 atoms. 23918 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1962 (Rfree = 0.000) for 11286 atoms. Found 30 (62 requested) and removed 74 (31 requested) atoms. Cycle 7: After refmac, R = 0.1882 (Rfree = 0.000) for 11151 atoms. Found 21 (61 requested) and removed 47 (30 requested) atoms. Cycle 8: After refmac, R = 0.1894 (Rfree = 0.000) for 11076 atoms. Found 32 (61 requested) and removed 59 (30 requested) atoms. Cycle 9: After refmac, R = 0.1827 (Rfree = 0.000) for 11020 atoms. Found 31 (60 requested) and removed 59 (30 requested) atoms. Cycle 10: After refmac, R = 0.1740 (Rfree = 0.000) for 10959 atoms. Found 25 (60 requested) and removed 58 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 11199 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 11219 seeds are put forward Round 1: 583 peptides, 118 chains. Longest chain 10 peptides. Score 0.286 Round 2: 660 peptides, 107 chains. Longest chain 16 peptides. Score 0.404 Round 3: 685 peptides, 112 chains. Longest chain 19 peptides. Score 0.407 Round 4: 685 peptides, 108 chains. Longest chain 14 peptides. Score 0.423 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Round 5: 708 peptides, 114 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 4 Chains 108, Residues 577, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26227 restraints for refining 11287 atoms. 24027 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1913 (Rfree = 0.000) for 11287 atoms. Found 48 (62 requested) and removed 55 (31 requested) atoms. Cycle 12: After refmac, R = 0.1927 (Rfree = 0.000) for 11214 atoms. Found 49 (62 requested) and removed 58 (31 requested) atoms. Cycle 13: After refmac, R = 0.1778 (Rfree = 0.000) for 11170 atoms. Found 28 (61 requested) and removed 54 (30 requested) atoms. Cycle 14: After refmac, R = 0.1702 (Rfree = 0.000) for 11120 atoms. Found 33 (61 requested) and removed 44 (30 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1341 (Rfree = 0.000) for 11075 atoms. Found 15 (61 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 11329 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 11341 seeds are put forward Round 1: 632 peptides, 125 chains. Longest chain 15 peptides. Score 0.305 Round 2: 689 peptides, 124 chains. Longest chain 20 peptides. Score 0.363 Round 3: 702 peptides, 116 chains. Longest chain 14 peptides. Score 0.407 Round 4: 724 peptides, 117 chains. Longest chain 15 peptides. Score 0.422 Round 5: 732 peptides, 115 chains. Longest chain 15 peptides. Score 0.437 Taking the results from Round 5 Chains 115, Residues 617, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26032 restraints for refining 11287 atoms. 23679 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1869 (Rfree = 0.000) for 11287 atoms. Found 47 (62 requested) and removed 55 (31 requested) atoms. Cycle 17: After refmac, R = 0.1784 (Rfree = 0.000) for 11221 atoms. Found 31 (62 requested) and removed 49 (31 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1729 (Rfree = 0.000) for 11176 atoms. Found 42 (61 requested) and removed 51 (30 requested) atoms. Cycle 19: After refmac, R = 0.1640 (Rfree = 0.000) for 11139 atoms. Found 30 (61 requested) and removed 39 (30 requested) atoms. Cycle 20: After refmac, R = 0.1332 (Rfree = 0.000) for 11117 atoms. Found 10 (61 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 11396 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11414 seeds are put forward Round 1: 609 peptides, 121 chains. Longest chain 10 peptides. Score 0.299 Round 2: 671 peptides, 110 chains. Longest chain 17 peptides. Score 0.402 Round 3: 683 peptides, 112 chains. Longest chain 17 peptides. Score 0.405 Round 4: 666 peptides, 105 chains. Longest chain 15 peptides. Score 0.417 Round 5: 667 peptides, 103 chains. Longest chain 16 peptides. Score 0.426 Taking the results from Round 5 Chains 103, Residues 564, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26525 restraints for refining 11287 atoms. 24372 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1829 (Rfree = 0.000) for 11287 atoms. Found 38 (62 requested) and removed 44 (31 requested) atoms. Cycle 22: After refmac, R = 0.1830 (Rfree = 0.000) for 11243 atoms. Found 50 (62 requested) and removed 49 (31 requested) atoms. Cycle 23: After refmac, R = 0.1737 (Rfree = 0.000) for 11206 atoms. Found 41 (61 requested) and removed 37 (30 requested) atoms. Cycle 24: After refmac, R = 0.1691 (Rfree = 0.000) for 11186 atoms. Found 35 (61 requested) and removed 45 (30 requested) atoms. Cycle 25: After refmac, R = 0.1645 (Rfree = 0.000) for 11158 atoms. Found 36 (61 requested) and removed 40 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.51 Search for helices and strands: 0 residues in 0 chains, 11386 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 11413 seeds are put forward Round 1: 562 peptides, 117 chains. Longest chain 11 peptides. Score 0.269 Round 2: 629 peptides, 110 chains. Longest chain 11 peptides. Score 0.364 Round 3: 650 peptides, 109 chains. Longest chain 14 peptides. Score 0.387 Round 4: 680 peptides, 108 chains. Longest chain 14 peptides. Score 0.418 Round 5: 666 peptides, 107 chains. Longest chain 13 peptides. Score 0.410 Taking the results from Round 4 Chains 108, Residues 572, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26277 restraints for refining 11287 atoms. 24097 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1903 (Rfree = 0.000) for 11287 atoms. Found 55 (62 requested) and removed 44 (31 requested) atoms. Cycle 27: After refmac, R = 0.1846 (Rfree = 0.000) for 11238 atoms. Found 52 (62 requested) and removed 45 (31 requested) atoms. Cycle 28: After refmac, R = 0.1742 (Rfree = 0.000) for 11207 atoms. Found 42 (61 requested) and removed 37 (30 requested) atoms. Cycle 29: After refmac, R = 0.1666 (Rfree = 0.000) for 11191 atoms. Found 44 (61 requested) and removed 38 (30 requested) atoms. Cycle 30: After refmac, R = 0.1273 (Rfree = 0.000) for 11186 atoms. Found 7 (61 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 11465 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 11481 seeds are put forward Round 1: 560 peptides, 119 chains. Longest chain 11 peptides. Score 0.258 Round 2: 594 peptides, 108 chains. Longest chain 12 peptides. Score 0.339 Round 3: 609 peptides, 107 chains. Longest chain 15 peptides. Score 0.357 Round 4: 612 peptides, 106 chains. Longest chain 13 peptides. Score 0.364 Round 5: 623 peptides, 106 chains. Longest chain 16 peptides. Score 0.374 Taking the results from Round 5 Chains 106, Residues 517, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 17103 reflections ( 95.07 % complete ) and 26692 restraints for refining 11286 atoms. 24730 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1916 (Rfree = 0.000) for 11286 atoms. Found 62 (62 requested) and removed 38 (31 requested) atoms. Cycle 32: After refmac, R = 0.1843 (Rfree = 0.000) for 11260 atoms. Found 62 (62 requested) and removed 47 (31 requested) atoms. Cycle 33: After refmac, R = 0.1799 (Rfree = 0.000) for 11245 atoms. Found 57 (62 requested) and removed 44 (31 requested) atoms. Cycle 34: After refmac, R = 0.1765 (Rfree = 0.000) for 11228 atoms. Found 61 (61 requested) and removed 35 (30 requested) atoms. Cycle 35: After refmac, R = 0.1383 (Rfree = 0.000) for 11234 atoms. Found 9 (61 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 11456 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 11474 seeds are put forward Round 1: 471 peptides, 102 chains. Longest chain 9 peptides. Score 0.239 Round 2: 575 peptides, 104 chains. Longest chain 13 peptides. Score 0.337 Round 3: 603 peptides, 110 chains. Longest chain 15 peptides. Score 0.339 Round 4: 598 peptides, 101 chains. Longest chain 14 peptides. Score 0.372 Round 5: 587 peptides, 99 chains. Longest chain 18 peptides. Score 0.369 Taking the results from Round 4 Chains 101, Residues 497, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26657 restraints for refining 11287 atoms. 24770 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1801 (Rfree = 0.000) for 11287 atoms. Found 50 (62 requested) and removed 43 (31 requested) atoms. Cycle 37: After refmac, R = 0.1758 (Rfree = 0.000) for 11257 atoms. Found 45 (62 requested) and removed 45 (31 requested) atoms. Cycle 38: After refmac, R = 0.1663 (Rfree = 0.000) for 11224 atoms. Found 33 (61 requested) and removed 33 (30 requested) atoms. Cycle 39: After refmac, R = 0.1676 (Rfree = 0.000) for 11198 atoms. Found 46 (61 requested) and removed 39 (30 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1607 (Rfree = 0.000) for 11187 atoms. Found 40 (61 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 11455 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 11468 seeds are put forward Round 1: 468 peptides, 102 chains. Longest chain 8 peptides. Score 0.235 Round 2: 499 peptides, 96 chains. Longest chain 10 peptides. Score 0.295 Round 3: 510 peptides, 90 chains. Longest chain 10 peptides. Score 0.333 Round 4: 528 peptides, 93 chains. Longest chain 13 peptides. Score 0.338 Round 5: 563 peptides, 97 chains. Longest chain 14 peptides. Score 0.355 Taking the results from Round 5 Chains 97, Residues 466, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17103 reflections ( 95.07 % complete ) and 26800 restraints for refining 11287 atoms. 25013 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1749 (Rfree = 0.000) for 11287 atoms. Found 40 (62 requested) and removed 37 (31 requested) atoms. Cycle 42: After refmac, R = 0.1780 (Rfree = 0.000) for 11255 atoms. Found 53 (62 requested) and removed 42 (31 requested) atoms. Cycle 43: After refmac, R = 0.1728 (Rfree = 0.000) for 11242 atoms. Found 60 (61 requested) and removed 43 (30 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1656 (Rfree = 0.000) for 11233 atoms. Found 50 (61 requested) and removed 36 (30 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1645 (Rfree = 0.000) for 11231 atoms. Found 61 (61 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 11477 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11496 seeds are put forward Round 1: 452 peptides, 100 chains. Longest chain 14 peptides. Score 0.227 Round 2: 516 peptides, 95 chains. Longest chain 13 peptides. Score 0.317 Round 3: 527 peptides, 96 chains. Longest chain 12 peptides. Score 0.324 Round 4: 534 peptides, 94 chains. Longest chain 17 peptides. Score 0.339 Round 5: 540 peptides, 97 chains. Longest chain 14 peptides. Score 0.333 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 94, Residues 440, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2awa-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17103 reflections ( 95.07 % complete ) and 26778 restraints for refining 11288 atoms. 25112 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1770 (Rfree = 0.000) for 11288 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.1779 (Rfree = 0.000) for 11207 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.1702 (Rfree = 0.000) for 11161 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.1641 (Rfree = 0.000) for 11118 atoms. TimeTaking 128.58