Mon 24 Dec 07:46:26 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 1vqy-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-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/1vqy-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-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 07:46:31 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/1vqy-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.4-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 795 and 0 Target number of residues in the AU: 795 Target solvent content: 0.5608 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-3.4-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 7424 target number of atoms Had to go as low as 0.65 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: 29.074 3.400 Wilson plot Bfac: 38.67 13838 reflections ( 98.37 % complete ) and 0 restraints for refining 8225 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3116 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2699 (Rfree = 0.000) for 8225 atoms. Found 56 (62 requested) and removed 76 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.89 2.93 Search for helices and strands: 0 residues in 0 chains, 8347 seeds are put forward NCS extension: 0 residues added, 8347 seeds are put forward Round 1: 405 peptides, 80 chains. Longest chain 10 peptides. Score 0.325 Round 2: 503 peptides, 84 chains. Longest chain 17 peptides. Score 0.456 Round 3: 520 peptides, 79 chains. Longest chain 17 peptides. Score 0.512 Round 4: 527 peptides, 82 chains. Longest chain 17 peptides. Score 0.504 Round 5: 549 peptides, 78 chains. Longest chain 24 peptides. Score 0.557 Taking the results from Round 5 Chains 79, Residues 471, Estimated correctness of the model 14.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14823 restraints for refining 6749 atoms. 12962 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2814 (Rfree = 0.000) for 6749 atoms. Found 50 (50 requested) and removed 50 (25 requested) atoms. Cycle 2: After refmac, R = 0.2382 (Rfree = 0.000) for 6697 atoms. Found 33 (50 requested) and removed 49 (25 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2341 (Rfree = 0.000) for 6657 atoms. Found 22 (50 requested) and removed 51 (25 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2351 (Rfree = 0.000) for 6595 atoms. Found 37 (50 requested) and removed 42 (25 requested) atoms. Cycle 5: After refmac, R = 0.2182 (Rfree = 0.000) for 6573 atoms. Found 22 (49 requested) and removed 35 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.90 2.94 Search for helices and strands: 0 residues in 0 chains, 6766 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 6779 seeds are put forward Round 1: 472 peptides, 82 chains. Longest chain 14 peptides. Score 0.421 Round 2: 530 peptides, 78 chains. Longest chain 17 peptides. Score 0.532 Round 3: 545 peptides, 81 chains. Longest chain 17 peptides. Score 0.535 Round 4: 549 peptides, 72 chains. Longest chain 19 peptides. Score 0.591 Round 5: 535 peptides, 77 chains. Longest chain 17 peptides. Score 0.545 Taking the results from Round 4 Chains 72, Residues 477, Estimated correctness of the model 25.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15045 restraints for refining 6750 atoms. 13209 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2595 (Rfree = 0.000) for 6750 atoms. Found 50 (50 requested) and removed 55 (25 requested) atoms. Cycle 7: After refmac, R = 0.2288 (Rfree = 0.000) for 6694 atoms. Found 20 (50 requested) and removed 39 (25 requested) atoms. Cycle 8: After refmac, R = 0.2066 (Rfree = 0.000) for 6654 atoms. Found 10 (50 requested) and removed 35 (25 requested) atoms. Cycle 9: After refmac, R = 0.2085 (Rfree = 0.000) for 6617 atoms. Found 22 (50 requested) and removed 45 (25 requested) atoms. Cycle 10: After refmac, R = 0.2054 (Rfree = 0.000) for 6587 atoms. Found 21 (49 requested) and removed 36 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.91 2.95 Search for helices and strands: 0 residues in 0 chains, 6805 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6823 seeds are put forward Round 1: 504 peptides, 88 chains. Longest chain 20 peptides. Score 0.431 Round 2: 549 peptides, 78 chains. Longest chain 19 peptides. Score 0.557 Round 3: 547 peptides, 77 chains. Longest chain 20 peptides. Score 0.560 Round 4: 574 peptides, 77 chains. Longest chain 20 peptides. Score 0.594 Round 5: 531 peptides, 74 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 4 Chains 78, Residues 497, Estimated correctness of the model 26.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14576 restraints for refining 6750 atoms. 12614 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2406 (Rfree = 0.000) for 6750 atoms. Found 28 (50 requested) and removed 46 (25 requested) atoms. Cycle 12: After refmac, R = 0.2222 (Rfree = 0.000) for 6700 atoms. Found 29 (50 requested) and removed 39 (25 requested) atoms. Cycle 13: After refmac, R = 0.2159 (Rfree = 0.000) for 6674 atoms. Found 27 (50 requested) and removed 44 (25 requested) atoms. Cycle 14: After refmac, R = 0.2129 (Rfree = 0.000) for 6643 atoms. Found 26 (50 requested) and removed 32 (25 requested) atoms. Cycle 15: After refmac, R = 0.2037 (Rfree = 0.000) for 6629 atoms. Found 17 (50 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.90 2.94 Search for helices and strands: 0 residues in 0 chains, 6825 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 6848 seeds are put forward Round 1: 469 peptides, 83 chains. Longest chain 19 peptides. Score 0.410 Round 2: 518 peptides, 71 chains. Longest chain 24 peptides. Score 0.557 Round 3: 521 peptides, 74 chains. Longest chain 18 peptides. Score 0.544 Round 4: 533 peptides, 75 chains. Longest chain 22 peptides. Score 0.554 Round 5: 516 peptides, 67 chains. Longest chain 20 peptides. Score 0.578 Taking the results from Round 5 Chains 67, Residues 449, Estimated correctness of the model 21.3 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14989 restraints for refining 6750 atoms. 13191 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2491 (Rfree = 0.000) for 6750 atoms. Found 37 (50 requested) and removed 49 (25 requested) atoms. Cycle 17: After refmac, R = 0.2483 (Rfree = 0.000) for 6712 atoms. Found 50 (50 requested) and removed 50 (25 requested) atoms. Cycle 18: After refmac, R = 0.2224 (Rfree = 0.000) for 6695 atoms. Found 43 (50 requested) and removed 30 (25 requested) atoms. Cycle 19: After refmac, R = 0.2160 (Rfree = 0.000) for 6692 atoms. Found 27 (50 requested) and removed 35 (25 requested) atoms. Cycle 20: After refmac, R = 0.2005 (Rfree = 0.000) for 6679 atoms. Found 18 (50 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 2.94 Search for helices and strands: 0 residues in 0 chains, 6877 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6894 seeds are put forward Round 1: 445 peptides, 78 chains. Longest chain 12 peptides. Score 0.406 Round 2: 520 peptides, 75 chains. Longest chain 23 peptides. Score 0.536 Round 3: 505 peptides, 72 chains. Longest chain 25 peptides. Score 0.534 Round 4: 505 peptides, 68 chains. Longest chain 22 peptides. Score 0.558 Round 5: 529 peptides, 69 chains. Longest chain 29 peptides. Score 0.583 Taking the results from Round 5 Chains 69, Residues 460, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15090 restraints for refining 6749 atoms. 13319 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2487 (Rfree = 0.000) for 6749 atoms. Found 47 (50 requested) and removed 42 (25 requested) atoms. Cycle 22: After refmac, R = 0.2294 (Rfree = 0.000) for 6725 atoms. Found 29 (50 requested) and removed 37 (25 requested) atoms. Cycle 23: After refmac, R = 0.2494 (Rfree = 0.000) for 6700 atoms. Found 50 (50 requested) and removed 70 (25 requested) atoms. Cycle 24: After refmac, R = 0.2268 (Rfree = 0.000) for 6666 atoms. Found 50 (50 requested) and removed 44 (25 requested) atoms. Cycle 25: After refmac, R = 0.2040 (Rfree = 0.000) for 6666 atoms. Found 27 (50 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.94 2.98 Search for helices and strands: 0 residues in 0 chains, 6878 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6895 seeds are put forward Round 1: 485 peptides, 84 chains. Longest chain 12 peptides. Score 0.428 Round 2: 510 peptides, 75 chains. Longest chain 16 peptides. Score 0.523 Round 3: 524 peptides, 75 chains. Longest chain 22 peptides. Score 0.542 Round 4: 538 peptides, 76 chains. Longest chain 16 peptides. Score 0.554 Round 5: 507 peptides, 71 chains. Longest chain 31 peptides. Score 0.543 Taking the results from Round 4 Chains 76, Residues 462, Estimated correctness of the model 13.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15025 restraints for refining 6750 atoms. 13253 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2600 (Rfree = 0.000) for 6750 atoms. Found 33 (50 requested) and removed 62 (25 requested) atoms. Cycle 27: After refmac, R = 0.2409 (Rfree = 0.000) for 6694 atoms. Found 50 (50 requested) and removed 48 (25 requested) atoms. Cycle 28: After refmac, R = 0.2389 (Rfree = 0.000) for 6679 atoms. Found 45 (50 requested) and removed 37 (25 requested) atoms. Cycle 29: After refmac, R = 0.2339 (Rfree = 0.000) for 6678 atoms. Found 43 (50 requested) and removed 47 (25 requested) atoms. Cycle 30: After refmac, R = 0.2111 (Rfree = 0.000) for 6664 atoms. Found 15 (50 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.87 2.91 Search for helices and strands: 0 residues in 0 chains, 6844 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6859 seeds are put forward Round 1: 421 peptides, 78 chains. Longest chain 12 peptides. Score 0.366 Round 2: 447 peptides, 77 chains. Longest chain 15 peptides. Score 0.416 Round 3: 444 peptides, 71 chains. Longest chain 19 peptides. Score 0.452 Round 4: 433 peptides, 63 chains. Longest chain 16 peptides. Score 0.488 Round 5: 449 peptides, 67 chains. Longest chain 15 peptides. Score 0.486 Taking the results from Round 4 Chains 63, Residues 370, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15463 restraints for refining 6749 atoms. 13968 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2516 (Rfree = 0.000) for 6749 atoms. Found 50 (50 requested) and removed 47 (25 requested) atoms. Cycle 32: After refmac, R = 0.2427 (Rfree = 0.000) for 6727 atoms. Found 50 (50 requested) and removed 46 (25 requested) atoms. Cycle 33: After refmac, R = 0.2456 (Rfree = 0.000) for 6715 atoms. Found 50 (50 requested) and removed 45 (25 requested) atoms. Cycle 34: After refmac, R = 0.2440 (Rfree = 0.000) for 6708 atoms. Found 50 (50 requested) and removed 39 (25 requested) atoms. Cycle 35: After refmac, R = 0.2502 (Rfree = 0.000) for 6707 atoms. Found 50 (50 requested) and removed 49 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.87 2.91 Search for helices and strands: 0 residues in 0 chains, 6889 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 6903 seeds are put forward Round 1: 374 peptides, 71 chains. Longest chain 13 peptides. Score 0.337 Round 2: 438 peptides, 73 chains. Longest chain 15 peptides. Score 0.429 Round 3: 472 peptides, 77 chains. Longest chain 14 peptides. Score 0.455 Round 4: 456 peptides, 76 chains. Longest chain 19 peptides. Score 0.437 Round 5: 452 peptides, 76 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 3 Chains 77, Residues 395, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15357 restraints for refining 6750 atoms. 13854 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2643 (Rfree = 0.000) for 6750 atoms. Found 35 (50 requested) and removed 49 (25 requested) atoms. Cycle 37: After refmac, R = 0.2637 (Rfree = 0.000) for 6710 atoms. Found 50 (50 requested) and removed 49 (25 requested) atoms. Cycle 38: After refmac, R = 0.2215 (Rfree = 0.000) for 6687 atoms. Found 28 (50 requested) and removed 31 (25 requested) atoms. Cycle 39: After refmac, R = 0.2059 (Rfree = 0.000) for 6668 atoms. Found 20 (50 requested) and removed 27 (25 requested) atoms. Cycle 40: After refmac, R = 0.2037 (Rfree = 0.000) for 6653 atoms. Found 16 (50 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 2.95 Search for helices and strands: 0 residues in 0 chains, 6802 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6815 seeds are put forward Round 1: 359 peptides, 68 chains. Longest chain 11 peptides. Score 0.333 Round 2: 406 peptides, 67 chains. Longest chain 12 peptides. Score 0.419 Round 3: 412 peptides, 65 chains. Longest chain 15 peptides. Score 0.443 Round 4: 417 peptides, 69 chains. Longest chain 13 peptides. Score 0.423 Round 5: 416 peptides, 65 chains. Longest chain 15 peptides. Score 0.449 Taking the results from Round 5 Chains 65, Residues 351, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15575 restraints for refining 6666 atoms. 14236 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2738 (Rfree = 0.000) for 6666 atoms. Found 50 (50 requested) and removed 70 (25 requested) atoms. Cycle 42: After refmac, R = 0.2539 (Rfree = 0.000) for 6623 atoms. Found 50 (50 requested) and removed 46 (25 requested) atoms. Cycle 43: After refmac, R = 0.2283 (Rfree = 0.000) for 6621 atoms. Found 37 (50 requested) and removed 35 (25 requested) atoms. Cycle 44: After refmac, R = 0.2560 (Rfree = 0.000) for 6619 atoms. Found 50 (50 requested) and removed 49 (25 requested) atoms. Cycle 45: After refmac, R = 0.2251 (Rfree = 0.000) for 6602 atoms. Found 36 (49 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 2.94 Search for helices and strands: 0 residues in 0 chains, 6778 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6802 seeds are put forward Round 1: 331 peptides, 65 chains. Longest chain 12 peptides. Score 0.305 Round 2: 388 peptides, 63 chains. Longest chain 16 peptides. Score 0.418 Round 3: 388 peptides, 62 chains. Longest chain 17 peptides. Score 0.425 Round 4: 404 peptides, 58 chains. Longest chain 13 peptides. Score 0.478 Round 5: 392 peptides, 64 chains. Longest chain 16 peptides. Score 0.418 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 346, 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 1vqy-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13838 reflections ( 98.37 % complete ) and 15064 restraints for refining 6591 atoms. 13738 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2645 (Rfree = 0.000) for 6591 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2669 (Rfree = 0.000) for 6555 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2401 (Rfree = 0.000) for 6522 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.2118 (Rfree = 0.000) for 6494 atoms. TimeTaking 69.22