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 1vqr-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-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/1vqr-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-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/1vqr-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-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 923 and 0 Target number of residues in the AU: 923 Target solvent content: 0.6017 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-3.4-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.75 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: 83.418 3.400 Wilson plot Bfac: 53.18 15170 reflections ( 88.81 % complete ) and 0 restraints for refining 10565 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3581 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3076 (Rfree = 0.000) for 10565 atoms. Found 71 (79 requested) and removed 144 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 10622 seeds are put forward NCS extension: 0 residues added, 10622 seeds are put forward Round 1: 317 peptides, 70 chains. Longest chain 8 peptides. Score 0.228 Round 2: 415 peptides, 88 chains. Longest chain 8 peptides. Score 0.264 Round 3: 418 peptides, 84 chains. Longest chain 10 peptides. Score 0.292 Round 4: 433 peptides, 85 chains. Longest chain 15 peptides. Score 0.308 Round 5: 445 peptides, 83 chains. Longest chain 16 peptides. Score 0.337 Taking the results from Round 5 Chains 83, Residues 362, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20786 restraints for refining 8638 atoms. 19401 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2493 (Rfree = 0.000) for 8638 atoms. Found 31 (65 requested) and removed 54 (32 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2322 (Rfree = 0.000) for 8543 atoms. Found 23 (65 requested) and removed 45 (32 requested) atoms. Cycle 3: After refmac, R = 0.2175 (Rfree = 0.000) for 8492 atoms. Found 23 (64 requested) and removed 40 (32 requested) atoms. Cycle 4: After refmac, R = 0.2080 (Rfree = 0.000) for 8447 atoms. Found 20 (63 requested) and removed 38 (31 requested) atoms. Cycle 5: After refmac, R = 0.2047 (Rfree = 0.000) for 8410 atoms. Found 10 (63 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 8591 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 8616 seeds are put forward Round 1: 403 peptides, 89 chains. Longest chain 8 peptides. Score 0.240 Round 2: 465 peptides, 91 chains. Longest chain 12 peptides. Score 0.317 Round 3: 461 peptides, 89 chains. Longest chain 12 peptides. Score 0.323 Round 4: 466 peptides, 87 chains. Longest chain 12 peptides. Score 0.342 Round 5: 464 peptides, 85 chains. Longest chain 11 peptides. Score 0.351 Taking the results from Round 5 Chains 85, Residues 379, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20761 restraints for refining 8555 atoms. 19314 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2294 (Rfree = 0.000) for 8555 atoms. Found 48 (64 requested) and removed 49 (32 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2083 (Rfree = 0.000) for 8522 atoms. Found 22 (64 requested) and removed 47 (32 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1987 (Rfree = 0.000) for 8467 atoms. Found 26 (64 requested) and removed 40 (32 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1891 (Rfree = 0.000) for 8432 atoms. Found 20 (63 requested) and removed 36 (31 requested) atoms. Cycle 10: After refmac, R = 0.1840 (Rfree = 0.000) for 8407 atoms. Found 22 (63 requested) and removed 46 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.11 Search for helices and strands: 0 residues in 0 chains, 8587 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8599 seeds are put forward Round 1: 424 peptides, 88 chains. Longest chain 12 peptides. Score 0.277 Round 2: 472 peptides, 83 chains. Longest chain 12 peptides. Score 0.373 Round 3: 468 peptides, 80 chains. Longest chain 11 peptides. Score 0.385 Round 4: 489 peptides, 82 chains. Longest chain 14 peptides. Score 0.401 Round 5: 483 peptides, 79 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 5 Chains 79, Residues 404, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20417 restraints for refining 8636 atoms. 18849 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2064 (Rfree = 0.000) for 8636 atoms. Found 43 (65 requested) and removed 49 (32 requested) atoms. Cycle 12: After refmac, R = 0.1906 (Rfree = 0.000) for 8614 atoms. Found 16 (65 requested) and removed 39 (32 requested) atoms. Cycle 13: After refmac, R = 0.1828 (Rfree = 0.000) for 8587 atoms. Found 12 (64 requested) and removed 37 (32 requested) atoms. Cycle 14: After refmac, R = 0.1796 (Rfree = 0.000) for 8560 atoms. Found 9 (64 requested) and removed 34 (32 requested) atoms. Cycle 15: After refmac, R = 0.1833 (Rfree = 0.000) for 8535 atoms. Found 16 (64 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 8743 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8756 seeds are put forward Round 1: 415 peptides, 88 chains. Longest chain 11 peptides. Score 0.264 Round 2: 465 peptides, 79 chains. Longest chain 12 peptides. Score 0.387 Round 3: 452 peptides, 77 chains. Longest chain 14 peptides. Score 0.381 Round 4: 464 peptides, 81 chains. Longest chain 12 peptides. Score 0.374 Round 5: 485 peptides, 83 chains. Longest chain 14 peptides. Score 0.390 Taking the results from Round 5 Chains 83, Residues 402, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20554 restraints for refining 8640 atoms. 19029 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2011 (Rfree = 0.000) for 8640 atoms. Found 44 (65 requested) and removed 39 (32 requested) atoms. Cycle 17: After refmac, R = 0.1895 (Rfree = 0.000) for 8616 atoms. Found 29 (65 requested) and removed 39 (32 requested) atoms. Cycle 18: After refmac, R = 0.1775 (Rfree = 0.000) for 8590 atoms. Found 19 (64 requested) and removed 35 (32 requested) atoms. Cycle 19: After refmac, R = 0.1724 (Rfree = 0.000) for 8564 atoms. Found 14 (64 requested) and removed 37 (32 requested) atoms. Cycle 20: After refmac, R = 0.1674 (Rfree = 0.000) for 8533 atoms. Found 17 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.16 Search for helices and strands: 0 residues in 0 chains, 8738 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8751 seeds are put forward Round 1: 443 peptides, 90 chains. Longest chain 10 peptides. Score 0.292 Round 2: 500 peptides, 91 chains. Longest chain 13 peptides. Score 0.365 Round 3: 505 peptides, 86 chains. Longest chain 16 peptides. Score 0.399 Round 4: 513 peptides, 88 chains. Longest chain 18 peptides. Score 0.399 Round 5: 496 peptides, 83 chains. Longest chain 14 peptides. Score 0.405 Taking the results from Round 5 Chains 83, Residues 413, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20367 restraints for refining 8641 atoms. 18744 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2023 (Rfree = 0.000) for 8641 atoms. Found 43 (65 requested) and removed 36 (32 requested) atoms. Cycle 22: After refmac, R = 0.1825 (Rfree = 0.000) for 8621 atoms. Found 12 (65 requested) and removed 36 (32 requested) atoms. Cycle 23: After refmac, R = 0.1761 (Rfree = 0.000) for 8590 atoms. Found 10 (64 requested) and removed 34 (32 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1748 (Rfree = 0.000) for 8561 atoms. Found 12 (64 requested) and removed 35 (32 requested) atoms. Cycle 25: After refmac, R = 0.1719 (Rfree = 0.000) for 8532 atoms. Found 16 (64 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.16 Search for helices and strands: 0 residues in 0 chains, 8703 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8722 seeds are put forward Round 1: 441 peptides, 86 chains. Longest chain 11 peptides. Score 0.313 Round 2: 479 peptides, 84 chains. Longest chain 16 peptides. Score 0.377 Round 3: 458 peptides, 82 chains. Longest chain 17 peptides. Score 0.360 Round 4: 475 peptides, 84 chains. Longest chain 14 peptides. Score 0.371 Round 5: 479 peptides, 84 chains. Longest chain 17 peptides. Score 0.377 Taking the results from Round 5 Chains 84, Residues 395, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20563 restraints for refining 8641 atoms. 19067 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1967 (Rfree = 0.000) for 8641 atoms. Found 42 (65 requested) and removed 36 (32 requested) atoms. Cycle 27: After refmac, R = 0.1806 (Rfree = 0.000) for 8633 atoms. Found 17 (65 requested) and removed 37 (32 requested) atoms. Cycle 28: After refmac, R = 0.1811 (Rfree = 0.000) for 8601 atoms. Found 21 (65 requested) and removed 38 (32 requested) atoms. Cycle 29: After refmac, R = 0.1785 (Rfree = 0.000) for 8575 atoms. Found 26 (64 requested) and removed 35 (32 requested) atoms. Cycle 30: After refmac, R = 0.1724 (Rfree = 0.000) for 8562 atoms. Found 10 (64 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.17 Search for helices and strands: 0 residues in 0 chains, 8728 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 8754 seeds are put forward Round 1: 438 peptides, 86 chains. Longest chain 11 peptides. Score 0.309 Round 2: 468 peptides, 82 chains. Longest chain 13 peptides. Score 0.374 Round 3: 498 peptides, 87 chains. Longest chain 13 peptides. Score 0.385 Round 4: 498 peptides, 83 chains. Longest chain 23 peptides. Score 0.407 Round 5: 496 peptides, 81 chains. Longest chain 18 peptides. Score 0.416 Taking the results from Round 5 Chains 81, Residues 415, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20344 restraints for refining 8641 atoms. 18746 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1957 (Rfree = 0.000) for 8641 atoms. Found 43 (65 requested) and removed 36 (32 requested) atoms. Cycle 32: After refmac, R = 0.1810 (Rfree = 0.000) for 8632 atoms. Found 10 (65 requested) and removed 33 (32 requested) atoms. Cycle 33: After refmac, R = 0.1805 (Rfree = 0.000) for 8599 atoms. Found 21 (64 requested) and removed 33 (32 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1755 (Rfree = 0.000) for 8582 atoms. Found 15 (64 requested) and removed 32 (32 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1684 (Rfree = 0.000) for 8559 atoms. Found 8 (64 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 8714 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 8731 seeds are put forward Round 1: 342 peptides, 69 chains. Longest chain 13 peptides. Score 0.274 Round 2: 378 peptides, 69 chains. Longest chain 16 peptides. Score 0.327 Round 3: 388 peptides, 68 chains. Longest chain 14 peptides. Score 0.347 Round 4: 418 peptides, 76 chains. Longest chain 14 peptides. Score 0.341 Round 5: 419 peptides, 70 chains. Longest chain 10 peptides. Score 0.378 Taking the results from Round 5 Chains 70, Residues 349, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20624 restraints for refining 8641 atoms. 19267 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1883 (Rfree = 0.000) for 8641 atoms. Found 41 (65 requested) and removed 35 (32 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1779 (Rfree = 0.000) for 8631 atoms. Found 20 (65 requested) and removed 36 (32 requested) atoms. Cycle 38: After refmac, R = 0.1782 (Rfree = 0.000) for 8605 atoms. Found 15 (65 requested) and removed 33 (32 requested) atoms. Cycle 39: After refmac, R = 0.1755 (Rfree = 0.000) for 8579 atoms. Found 21 (64 requested) and removed 33 (32 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1749 (Rfree = 0.000) for 8562 atoms. Found 15 (64 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 8739 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8751 seeds are put forward Round 1: 359 peptides, 77 chains. Longest chain 9 peptides. Score 0.249 Round 2: 405 peptides, 73 chains. Longest chain 11 peptides. Score 0.341 Round 3: 414 peptides, 71 chains. Longest chain 14 peptides. Score 0.365 Round 4: 401 peptides, 72 chains. Longest chain 12 peptides. Score 0.341 Round 5: 405 peptides, 70 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 3 Chains 71, Residues 343, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20632 restraints for refining 8640 atoms. 19299 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1836 (Rfree = 0.000) for 8640 atoms. Found 40 (65 requested) and removed 35 (32 requested) atoms. Cycle 42: After refmac, R = 0.1754 (Rfree = 0.000) for 8636 atoms. Found 23 (65 requested) and removed 34 (32 requested) atoms. Cycle 43: After refmac, R = 0.1743 (Rfree = 0.000) for 8621 atoms. Found 22 (65 requested) and removed 33 (32 requested) atoms. Cycle 44: After refmac, R = 0.1743 (Rfree = 0.000) for 8601 atoms. Found 16 (64 requested) and removed 32 (32 requested) atoms. Cycle 45: After refmac, R = 0.1700 (Rfree = 0.000) for 8577 atoms. Found 13 (64 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.17 Search for helices and strands: 0 residues in 0 chains, 8761 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 8783 seeds are put forward Round 1: 353 peptides, 76 chains. Longest chain 8 peptides. Score 0.246 Round 2: 386 peptides, 71 chains. Longest chain 13 peptides. Score 0.326 Round 3: 366 peptides, 67 chains. Longest chain 12 peptides. Score 0.322 Round 4: 378 peptides, 64 chains. Longest chain 14 peptides. Score 0.358 Round 5: 404 peptides, 67 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 337, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input Building loops using Loopy2018 67 chains (337 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15170 reflections ( 88.81 % complete ) and 20598 restraints for refining 8640 atoms. 19292 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1862 (Rfree = 0.000) for 8640 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1776 (Rfree = 0.000) for 8599 atoms. Found 0 (64 requested) and removed 20 (32 requested) atoms. Cycle 48: After refmac, R = 0.1750 (Rfree = 0.000) for 8574 atoms. Found 0 (64 requested) and removed 12 (32 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1713 (Rfree = 0.000) for 8555 atoms. Found 0 (64 requested) and removed 5 (32 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 122.73