null Tue 25 Dec 19:27:55 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 2f4l-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-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/2f4l-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-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 19:28:05 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/2f4l-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-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 850 and 0 Target number of residues in the AU: 850 Target solvent content: 0.6436 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: 0.50 Input MTZ file: 2f4l-3.6-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.70 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: 86.372 3.600 Wilson plot Bfac: 74.06 15528 reflections ( 99.66 % complete ) and 0 restraints for refining 10546 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3007 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2860 (Rfree = 0.000) for 10546 atoms. Found 67 (67 requested) and removed 120 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 10623 seeds are put forward NCS extension: 0 residues added, 10623 seeds are put forward Round 1: 592 peptides, 97 chains. Longest chain 13 peptides. Score 0.442 Round 2: 750 peptides, 90 chains. Longest chain 29 peptides. Score 0.634 Round 3: 794 peptides, 82 chains. Longest chain 34 peptides. Score 0.698 Round 4: 813 peptides, 75 chains. Longest chain 31 peptides. Score 0.734 Round 5: 845 peptides, 84 chains. Longest chain 39 peptides. Score 0.727 Taking the results from Round 4 Chains 89, Residues 738, Estimated correctness of the model 59.5 % 14 chains (151 residues) have been docked in sequence Building loops using Loopy2018 89 chains (738 residues) following loop building 14 chains (151 residues) in sequence following loop building ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 17182 restraints for refining 8614 atoms. 13825 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2448 (Rfree = 0.000) for 8614 atoms. Found 52 (55 requested) and removed 107 (27 requested) atoms. Cycle 2: After refmac, R = 0.2333 (Rfree = 0.000) for 8395 atoms. Found 26 (53 requested) and removed 51 (27 requested) atoms. Cycle 3: After refmac, R = 0.2238 (Rfree = 0.000) for 8302 atoms. Found 21 (51 requested) and removed 47 (26 requested) atoms. Cycle 4: After refmac, R = 0.2187 (Rfree = 0.000) for 8221 atoms. Found 28 (50 requested) and removed 49 (26 requested) atoms. Cycle 5: After refmac, R = 0.2131 (Rfree = 0.000) for 8171 atoms. Found 25 (48 requested) and removed 44 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 8342 seeds are put forward NCS extension: 11 residues added (18 deleted due to clashes), 8353 seeds are put forward Round 1: 712 peptides, 88 chains. Longest chain 30 peptides. Score 0.609 Round 2: 771 peptides, 82 chains. Longest chain 32 peptides. Score 0.681 Round 3: 816 peptides, 81 chains. Longest chain 39 peptides. Score 0.717 Round 4: 812 peptides, 74 chains. Longest chain 37 peptides. Score 0.736 Round 5: 815 peptides, 71 chains. Longest chain 41 peptides. Score 0.748 Taking the results from Round 5 Chains 80, Residues 744, Estimated correctness of the model 63.4 % 15 chains (226 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 192 B and 198 B 80 chains (741 residues) following loop building 14 chains (231 residues) in sequence following loop building ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 16500 restraints for refining 8615 atoms. 12878 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2486 (Rfree = 0.000) for 8615 atoms. Found 49 (49 requested) and removed 96 (27 requested) atoms. Cycle 7: After refmac, R = 0.2268 (Rfree = 0.000) for 8481 atoms. Found 36 (48 requested) and removed 54 (27 requested) atoms. Cycle 8: After refmac, R = 0.2124 (Rfree = 0.000) for 8416 atoms. Found 29 (46 requested) and removed 51 (27 requested) atoms. Cycle 9: After refmac, R = 0.2042 (Rfree = 0.000) for 8370 atoms. Found 18 (45 requested) and removed 37 (26 requested) atoms. Cycle 10: After refmac, R = 0.2002 (Rfree = 0.000) for 8338 atoms. Found 17 (43 requested) and removed 38 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 8476 seeds are put forward NCS extension: 23 residues added (10 deleted due to clashes), 8499 seeds are put forward Round 1: 735 peptides, 99 chains. Longest chain 31 peptides. Score 0.584 Round 2: 751 peptides, 85 chains. Longest chain 31 peptides. Score 0.654 Round 3: 786 peptides, 85 chains. Longest chain 35 peptides. Score 0.682 Round 4: 779 peptides, 85 chains. Longest chain 41 peptides. Score 0.676 Round 5: 770 peptides, 80 chains. Longest chain 27 peptides. Score 0.687 Taking the results from Round 5 Chains 84, Residues 690, Estimated correctness of the model 45.5 % 6 chains (84 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18360 restraints for refining 8613 atoms. 15387 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2428 (Rfree = 0.000) for 8613 atoms. Found 44 (44 requested) and removed 57 (27 requested) atoms. Cycle 12: After refmac, R = 0.2233 (Rfree = 0.000) for 8538 atoms. Found 32 (44 requested) and removed 37 (27 requested) atoms. Cycle 13: After refmac, R = 0.2150 (Rfree = 0.000) for 8509 atoms. Found 31 (43 requested) and removed 33 (27 requested) atoms. Cycle 14: After refmac, R = 0.2151 (Rfree = 0.000) for 8488 atoms. Found 30 (43 requested) and removed 38 (27 requested) atoms. Cycle 15: After refmac, R = 0.2079 (Rfree = 0.000) for 8461 atoms. Found 34 (43 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 8599 seeds are put forward NCS extension: 19 residues added (10 deleted due to clashes), 8618 seeds are put forward Round 1: 639 peptides, 89 chains. Longest chain 23 peptides. Score 0.533 Round 2: 722 peptides, 88 chains. Longest chain 41 peptides. Score 0.618 Round 3: 710 peptides, 82 chains. Longest chain 25 peptides. Score 0.631 Round 4: 750 peptides, 87 chains. Longest chain 32 peptides. Score 0.646 Round 5: 760 peptides, 86 chains. Longest chain 25 peptides. Score 0.658 Taking the results from Round 5 Chains 90, Residues 674, Estimated correctness of the model 35.9 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18953 restraints for refining 8611 atoms. 16245 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2466 (Rfree = 0.000) for 8611 atoms. Found 44 (44 requested) and removed 44 (27 requested) atoms. Cycle 17: After refmac, R = 0.2426 (Rfree = 0.000) for 8536 atoms. Found 44 (44 requested) and removed 46 (27 requested) atoms. Cycle 18: After refmac, R = 0.2252 (Rfree = 0.000) for 8471 atoms. Found 43 (43 requested) and removed 39 (27 requested) atoms. Cycle 19: After refmac, R = 0.2241 (Rfree = 0.000) for 8437 atoms. Found 43 (43 requested) and removed 36 (27 requested) atoms. Cycle 20: After refmac, R = 0.1864 (Rfree = 0.000) for 8416 atoms. Found 32 (43 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.48 Search for helices and strands: 0 residues in 0 chains, 8649 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 8668 seeds are put forward Round 1: 602 peptides, 100 chains. Longest chain 13 peptides. Score 0.439 Round 2: 653 peptides, 82 chains. Longest chain 30 peptides. Score 0.579 Round 3: 709 peptides, 89 chains. Longest chain 23 peptides. Score 0.602 Round 4: 703 peptides, 82 chains. Longest chain 30 peptides. Score 0.625 Round 5: 709 peptides, 87 chains. Longest chain 31 peptides. Score 0.610 Taking the results from Round 4 Chains 87, Residues 621, Estimated correctness of the model 24.2 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18951 restraints for refining 8576 atoms. 16394 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2431 (Rfree = 0.000) for 8576 atoms. Found 44 (44 requested) and removed 68 (27 requested) atoms. Cycle 22: After refmac, R = 0.2247 (Rfree = 0.000) for 8495 atoms. Found 43 (43 requested) and removed 38 (27 requested) atoms. Cycle 23: After refmac, R = 0.2146 (Rfree = 0.000) for 8473 atoms. Found 35 (43 requested) and removed 33 (27 requested) atoms. Cycle 24: After refmac, R = 0.2077 (Rfree = 0.000) for 8456 atoms. Found 43 (43 requested) and removed 35 (27 requested) atoms. Cycle 25: After refmac, R = 0.2097 (Rfree = 0.000) for 8445 atoms. Found 40 (43 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.49 Search for helices and strands: 0 residues in 0 chains, 8584 seeds are put forward NCS extension: 27 residues added (17 deleted due to clashes), 8611 seeds are put forward Round 1: 610 peptides, 98 chains. Longest chain 22 peptides. Score 0.458 Round 2: 681 peptides, 88 chains. Longest chain 31 peptides. Score 0.580 Round 3: 724 peptides, 88 chains. Longest chain 28 peptides. Score 0.619 Round 4: 742 peptides, 90 chains. Longest chain 34 peptides. Score 0.627 Round 5: 707 peptides, 83 chains. Longest chain 31 peptides. Score 0.625 Taking the results from Round 4 Chains 94, Residues 652, Estimated correctness of the model 24.9 % 9 chains (66 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18813 restraints for refining 8613 atoms. 16088 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2332 (Rfree = 0.000) for 8613 atoms. Found 44 (44 requested) and removed 51 (27 requested) atoms. Cycle 27: After refmac, R = 0.2186 (Rfree = 0.000) for 8553 atoms. Found 44 (44 requested) and removed 34 (27 requested) atoms. Cycle 28: After refmac, R = 0.2056 (Rfree = 0.000) for 8538 atoms. Found 34 (43 requested) and removed 34 (27 requested) atoms. Cycle 29: After refmac, R = 0.2086 (Rfree = 0.000) for 8520 atoms. Found 30 (43 requested) and removed 36 (27 requested) atoms. Cycle 30: After refmac, R = 0.1982 (Rfree = 0.000) for 8498 atoms. Found 32 (43 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 8656 seeds are put forward NCS extension: 40 residues added (7 deleted due to clashes), 8696 seeds are put forward Round 1: 586 peptides, 97 chains. Longest chain 24 peptides. Score 0.435 Round 2: 649 peptides, 88 chains. Longest chain 28 peptides. Score 0.548 Round 3: 678 peptides, 92 chains. Longest chain 26 peptides. Score 0.559 Round 4: 679 peptides, 82 chains. Longest chain 41 peptides. Score 0.603 Round 5: 662 peptides, 82 chains. Longest chain 35 peptides. Score 0.588 Taking the results from Round 4 Chains 86, Residues 597, Estimated correctness of the model 15.8 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19387 restraints for refining 8612 atoms. 16929 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2291 (Rfree = 0.000) for 8612 atoms. Found 44 (44 requested) and removed 43 (27 requested) atoms. Cycle 32: After refmac, R = 0.2178 (Rfree = 0.000) for 8583 atoms. Found 44 (44 requested) and removed 39 (27 requested) atoms. Cycle 33: After refmac, R = 0.2176 (Rfree = 0.000) for 8577 atoms. Found 44 (44 requested) and removed 37 (27 requested) atoms. Cycle 34: After refmac, R = 0.2090 (Rfree = 0.000) for 8576 atoms. Found 37 (44 requested) and removed 36 (27 requested) atoms. Cycle 35: After refmac, R = 0.2075 (Rfree = 0.000) for 8566 atoms. Found 44 (44 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 8716 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 8741 seeds are put forward Round 1: 565 peptides, 95 chains. Longest chain 23 peptides. Score 0.420 Round 2: 603 peptides, 80 chains. Longest chain 27 peptides. Score 0.538 Round 3: 613 peptides, 81 chains. Longest chain 19 peptides. Score 0.543 Round 4: 651 peptides, 82 chains. Longest chain 36 peptides. Score 0.577 Round 5: 621 peptides, 82 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 4 Chains 86, Residues 569, Estimated correctness of the model 5.5 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19855 restraints for refining 8615 atoms. 17601 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2226 (Rfree = 0.000) for 8615 atoms. Found 44 (44 requested) and removed 40 (27 requested) atoms. Cycle 37: After refmac, R = 0.2128 (Rfree = 0.000) for 8603 atoms. Found 44 (44 requested) and removed 38 (27 requested) atoms. Cycle 38: After refmac, R = 0.2107 (Rfree = 0.000) for 8595 atoms. Found 38 (44 requested) and removed 31 (27 requested) atoms. Cycle 39: After refmac, R = 0.1979 (Rfree = 0.000) for 8590 atoms. Found 32 (44 requested) and removed 31 (27 requested) atoms. Cycle 40: After refmac, R = 0.2031 (Rfree = 0.000) for 8584 atoms. Found 40 (44 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 8769 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 8789 seeds are put forward Round 1: 534 peptides, 91 chains. Longest chain 18 peptides. Score 0.404 Round 2: 596 peptides, 86 chains. Longest chain 23 peptides. Score 0.502 Round 3: 597 peptides, 84 chains. Longest chain 24 peptides. Score 0.512 Round 4: 641 peptides, 87 chains. Longest chain 24 peptides. Score 0.545 Round 5: 637 peptides, 81 chains. Longest chain 36 peptides. Score 0.568 Taking the results from Round 5 Chains 86, Residues 556, Estimated correctness of the model 1.7 % 8 chains (81 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19383 restraints for refining 8614 atoms. 16928 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2671 (Rfree = 0.000) for 8614 atoms. Found 44 (44 requested) and removed 41 (27 requested) atoms. Cycle 42: After refmac, R = 0.2454 (Rfree = 0.000) for 8562 atoms. Found 44 (44 requested) and removed 36 (27 requested) atoms. Cycle 43: After refmac, R = 0.2081 (Rfree = 0.000) for 8523 atoms. Found 32 (43 requested) and removed 32 (27 requested) atoms. Cycle 44: After refmac, R = 0.2001 (Rfree = 0.000) for 8492 atoms. Found 22 (43 requested) and removed 32 (27 requested) atoms. Cycle 45: After refmac, R = 0.1949 (Rfree = 0.000) for 8469 atoms. Found 25 (43 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 8612 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8628 seeds are put forward Round 1: 511 peptides, 89 chains. Longest chain 17 peptides. Score 0.386 Round 2: 580 peptides, 92 chains. Longest chain 21 peptides. Score 0.454 Round 3: 560 peptides, 82 chains. Longest chain 21 peptides. Score 0.481 Round 4: 562 peptides, 78 chains. Longest chain 25 peptides. Score 0.503 Round 5: 563 peptides, 80 chains. Longest chain 23 peptides. Score 0.495 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 81, Residues 484, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 81 chains (484 residues) following loop building 4 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15528 reflections ( 99.66 % complete ) and 20231 restraints for refining 8614 atoms. 18286 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2199 (Rfree = 0.000) for 8614 atoms. Found 0 (44 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2180 (Rfree = 0.000) for 8553 atoms. Found 0 (44 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.2181 (Rfree = 0.000) for 8509 atoms. Found 0 (43 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2200 (Rfree = 0.000) for 8471 atoms. Found 0 (43 requested) and removed 27 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:30:16 GMT 2018 Job finished. TimeTaking 122.35 Used memory is bytes: 27307280