Mon 24 Dec 00:13:07 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2awa-2.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-2.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-2.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-parrot-mrncs ############### 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 00:13:12 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/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-2.7-parrot-mrncs/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 1347 and 0 Target number of residues in the AU: 1347 Target solvent content: 0.5978 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-2.7-parrot-mrncs.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-2.7-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12480 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. 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 2.690 Wilson plot Bfac: 51.62 48746 reflections ( 97.20 % complete ) and 0 restraints for refining 13826 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Starting model: R = 0.3711 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2841 (Rfree = 0.000) for 13826 atoms. Found 74 (203 requested) and removed 154 (101 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.80 2.69 NCS extension: 0 residues added, 13746 seeds are put forward Round 1: 661 peptides, 136 chains. Longest chain 9 peptides. Score 0.288 Round 2: 756 peptides, 137 chains. Longest chain 15 peptides. Score 0.374 Round 3: 781 peptides, 133 chains. Longest chain 16 peptides. Score 0.411 Round 4: 827 peptides, 139 chains. Longest chain 19 peptides. Score 0.428 Round 5: 827 peptides, 136 chains. Longest chain 17 peptides. Score 0.439 Taking the results from Round 5 Chains 136, Residues 691, Estimated correctness of the model 36.7 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 25451 restraints for refining 11585 atoms. 22798 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2994 (Rfree = 0.000) for 11585 atoms. Found 112 (170 requested) and removed 110 (85 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.3062 (Rfree = 0.000) for 11521 atoms. Found 158 (170 requested) and removed 101 (85 requested) atoms. Cycle 3: After refmac, R = 0.3014 (Rfree = 0.000) for 11516 atoms. Found 161 (170 requested) and removed 102 (85 requested) atoms. Cycle 4: After refmac, R = 0.2950 (Rfree = 0.000) for 11532 atoms. Found 155 (170 requested) and removed 102 (85 requested) atoms. Cycle 5: After refmac, R = 0.2968 (Rfree = 0.000) for 11551 atoms. Found 170 (170 requested) and removed 97 (85 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.84 2.73 NCS extension: 10 residues added (1 deleted due to clashes), 11840 seeds are put forward Round 1: 728 peptides, 140 chains. Longest chain 12 peptides. Score 0.336 Round 2: 789 peptides, 134 chains. Longest chain 21 peptides. Score 0.414 Round 3: 822 peptides, 136 chains. Longest chain 20 peptides. Score 0.435 Round 4: 827 peptides, 129 chains. Longest chain 18 peptides. Score 0.465 Round 5: 818 peptides, 133 chains. Longest chain 22 peptides. Score 0.443 Taking the results from Round 4 Chains 129, Residues 698, Estimated correctness of the model 42.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 25124 restraints for refining 11585 atoms. 22461 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2926 (Rfree = 0.000) for 11585 atoms. Found 129 (170 requested) and removed 103 (85 requested) atoms. Cycle 7: After refmac, R = 0.2816 (Rfree = 0.000) for 11549 atoms. Found 162 (170 requested) and removed 101 (85 requested) atoms. Cycle 8: After refmac, R = 0.2729 (Rfree = 0.000) for 11576 atoms. Found 142 (170 requested) and removed 93 (85 requested) atoms. Cycle 9: After refmac, R = 0.2699 (Rfree = 0.000) for 11591 atoms. Found 149 (171 requested) and removed 91 (85 requested) atoms. Cycle 10: After refmac, R = 0.2641 (Rfree = 0.000) for 11626 atoms. Found 164 (171 requested) and removed 93 (85 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.82 2.71 NCS extension: 29 residues added (1 deleted due to clashes), 11891 seeds are put forward Round 1: 716 peptides, 133 chains. Longest chain 14 peptides. Score 0.353 Round 2: 822 peptides, 136 chains. Longest chain 15 peptides. Score 0.435 Round 3: 858 peptides, 131 chains. Longest chain 19 peptides. Score 0.483 Round 4: 857 peptides, 130 chains. Longest chain 22 peptides. Score 0.485 Round 5: 840 peptides, 136 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 4 Chains 131, Residues 727, Estimated correctness of the model 45.9 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 23956 restraints for refining 11585 atoms. 21123 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2659 (Rfree = 0.000) for 11585 atoms. Found 115 (170 requested) and removed 99 (85 requested) atoms. Cycle 12: After refmac, R = 0.2593 (Rfree = 0.000) for 11566 atoms. Found 153 (170 requested) and removed 93 (85 requested) atoms. Cycle 13: After refmac, R = 0.2566 (Rfree = 0.000) for 11606 atoms. Found 127 (171 requested) and removed 93 (85 requested) atoms. Cycle 14: After refmac, R = 0.2507 (Rfree = 0.000) for 11620 atoms. Found 140 (171 requested) and removed 98 (85 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2462 (Rfree = 0.000) for 11641 atoms. Found 120 (171 requested) and removed 90 (85 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.81 2.70 NCS extension: 48 residues added (6 deleted due to clashes), 11869 seeds are put forward Round 1: 757 peptides, 137 chains. Longest chain 17 peptides. Score 0.375 Round 2: 821 peptides, 128 chains. Longest chain 18 peptides. Score 0.463 Round 3: 821 peptides, 126 chains. Longest chain 19 peptides. Score 0.471 Round 4: 853 peptides, 123 chains. Longest chain 20 peptides. Score 0.506 Round 5: 846 peptides, 129 chains. Longest chain 21 peptides. Score 0.480 Taking the results from Round 4 Chains 123, Residues 730, Estimated correctness of the model 49.9 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 48746 reflections ( 97.20 % complete ) and 23801 restraints for refining 11585 atoms. 20936 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2548 (Rfree = 0.000) for 11585 atoms. Found 144 (170 requested) and removed 90 (85 requested) atoms. Cycle 17: After refmac, R = 0.2471 (Rfree = 0.000) for 11609 atoms. Found 153 (171 requested) and removed 91 (85 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2434 (Rfree = 0.000) for 11644 atoms. Found 171 (171 requested) and removed 89 (85 requested) atoms. Cycle 19: After refmac, R = 0.2438 (Rfree = 0.000) for 11705 atoms. Found 172 (172 requested) and removed 90 (86 requested) atoms. Cycle 20: After refmac, R = 0.2437 (Rfree = 0.000) for 11760 atoms. Found 161 (173 requested) and removed 90 (86 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.81 2.70 NCS extension: 3 residues added (0 deleted due to clashes), 11957 seeds are put forward Round 1: 717 peptides, 128 chains. Longest chain 17 peptides. Score 0.373 Round 2: 755 peptides, 120 chains. Longest chain 20 peptides. Score 0.437 Round 3: 781 peptides, 119 chains. Longest chain 23 peptides. Score 0.463 Round 4: 801 peptides, 121 chains. Longest chain 19 peptides. Score 0.472 Round 5: 818 peptides, 120 chains. Longest chain 28 peptides. Score 0.489 Taking the results from Round 5 Chains 121, Residues 698, Estimated correctness of the model 46.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 23926 restraints for refining 11585 atoms. 21212 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2564 (Rfree = 0.000) for 11585 atoms. Found 131 (170 requested) and removed 88 (85 requested) atoms. Cycle 22: After refmac, R = 0.2511 (Rfree = 0.000) for 11595 atoms. Found 158 (171 requested) and removed 88 (85 requested) atoms. Cycle 23: After refmac, R = 0.2487 (Rfree = 0.000) for 11646 atoms. Found 171 (171 requested) and removed 92 (85 requested) atoms. Cycle 24: After refmac, R = 0.2470 (Rfree = 0.000) for 11712 atoms. Found 161 (172 requested) and removed 86 (86 requested) atoms. Cycle 25: After refmac, R = 0.2507 (Rfree = 0.000) for 11766 atoms. Found 172 (173 requested) and removed 89 (86 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.83 2.72 NCS extension: 34 residues added (0 deleted due to clashes), 12010 seeds are put forward Round 1: 718 peptides, 126 chains. Longest chain 19 peptides. Score 0.382 Round 2: 771 peptides, 125 chains. Longest chain 20 peptides. Score 0.432 Round 3: 802 peptides, 122 chains. Longest chain 23 peptides. Score 0.469 Round 4: 826 peptides, 127 chains. Longest chain 18 peptides. Score 0.471 Round 5: 827 peptides, 121 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 5 Chains 121, Residues 706, Estimated correctness of the model 47.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24006 restraints for refining 11586 atoms. 21303 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2596 (Rfree = 0.000) for 11586 atoms. Found 155 (170 requested) and removed 88 (85 requested) atoms. Cycle 27: After refmac, R = 0.2500 (Rfree = 0.000) for 11626 atoms. Found 154 (171 requested) and removed 89 (85 requested) atoms. Cycle 28: After refmac, R = 0.2489 (Rfree = 0.000) for 11670 atoms. Found 126 (172 requested) and removed 95 (86 requested) atoms. Cycle 29: After refmac, R = 0.2444 (Rfree = 0.000) for 11687 atoms. Found 133 (172 requested) and removed 93 (86 requested) atoms. Cycle 30: After refmac, R = 0.2427 (Rfree = 0.000) for 11710 atoms. Found 158 (172 requested) and removed 90 (86 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.81 2.70 NCS extension: 0 residues added, 11890 seeds are put forward Round 1: 703 peptides, 127 chains. Longest chain 13 peptides. Score 0.364 Round 2: 749 peptides, 120 chains. Longest chain 15 peptides. Score 0.432 Round 3: 760 peptides, 116 chains. Longest chain 19 peptides. Score 0.456 Round 4: 775 peptides, 113 chains. Longest chain 22 peptides. Score 0.480 Round 5: 777 peptides, 114 chains. Longest chain 20 peptides. Score 0.478 Taking the results from Round 4 Chains 113, Residues 662, Estimated correctness of the model 44.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 24059 restraints for refining 11585 atoms. 21524 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2504 (Rfree = 0.000) for 11585 atoms. Found 130 (170 requested) and removed 89 (85 requested) atoms. Cycle 32: After refmac, R = 0.2457 (Rfree = 0.000) for 11609 atoms. Found 136 (171 requested) and removed 89 (85 requested) atoms. Cycle 33: After refmac, R = 0.2460 (Rfree = 0.000) for 11643 atoms. Found 165 (171 requested) and removed 90 (85 requested) atoms. Cycle 34: After refmac, R = 0.2062 (Rfree = 0.000) for 11708 atoms. Found 53 (172 requested) and removed 88 (86 requested) atoms. Cycle 35: After refmac, R = 0.1958 (Rfree = 0.000) for 11666 atoms. Found 37 (171 requested) and removed 88 (85 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.81 2.70 NCS extension: 24 residues added (1 deleted due to clashes), 11737 seeds are put forward Round 1: 672 peptides, 121 chains. Longest chain 12 peptides. Score 0.360 Round 2: 770 peptides, 113 chains. Longest chain 18 peptides. Score 0.476 Round 3: 759 peptides, 116 chains. Longest chain 17 peptides. Score 0.456 Round 4: 773 peptides, 110 chains. Longest chain 21 peptides. Score 0.489 Round 5: 760 peptides, 116 chains. Longest chain 18 peptides. Score 0.456 Taking the results from Round 4 Chains 110, Residues 663, Estimated correctness of the model 46.7 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 23849 restraints for refining 11586 atoms. 21263 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2482 (Rfree = 0.000) for 11586 atoms. Found 151 (170 requested) and removed 94 (85 requested) atoms. Cycle 37: After refmac, R = 0.2450 (Rfree = 0.000) for 11624 atoms. Found 171 (171 requested) and removed 88 (85 requested) atoms. Cycle 38: After refmac, R = 0.2070 (Rfree = 0.000) for 11686 atoms. Found 75 (172 requested) and removed 90 (86 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1971 (Rfree = 0.000) for 11661 atoms. Found 44 (171 requested) and removed 87 (85 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1949 (Rfree = 0.000) for 11612 atoms. Found 36 (171 requested) and removed 85 (85 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.82 2.71 NCS extension: 13 residues added (0 deleted due to clashes), 11643 seeds are put forward Round 1: 675 peptides, 125 chains. Longest chain 14 peptides. Score 0.346 Round 2: 730 peptides, 114 chains. Longest chain 16 peptides. Score 0.439 Round 3: 735 peptides, 109 chains. Longest chain 17 peptides. Score 0.461 Round 4: 740 peptides, 110 chains. Longest chain 16 peptides. Score 0.462 Round 5: 761 peptides, 111 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 5 Chains 112, Residues 650, Estimated correctness of the model 44.2 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 48746 reflections ( 97.20 % complete ) and 23683 restraints for refining 11585 atoms. 21143 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2374 (Rfree = 0.000) for 11585 atoms. Found 137 (170 requested) and removed 91 (85 requested) atoms. Cycle 42: After refmac, R = 0.2374 (Rfree = 0.000) for 11615 atoms. Found 146 (171 requested) and removed 91 (85 requested) atoms. Cycle 43: After refmac, R = 0.2014 (Rfree = 0.000) for 11654 atoms. Found 72 (171 requested) and removed 86 (85 requested) atoms. Cycle 44: After refmac, R = 0.1913 (Rfree = 0.000) for 11632 atoms. Found 35 (171 requested) and removed 85 (85 requested) atoms. Cycle 45: After refmac, R = 0.1900 (Rfree = 0.000) for 11579 atoms. Found 31 (170 requested) and removed 85 (85 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.83 2.72 NCS extension: 10 residues added (2 deleted due to clashes), 11587 seeds are put forward Round 1: 682 peptides, 125 chains. Longest chain 14 peptides. Score 0.353 Round 2: 741 peptides, 116 chains. Longest chain 16 peptides. Score 0.440 Round 3: 719 peptides, 111 chains. Longest chain 16 peptides. Score 0.440 Round 4: 737 peptides, 113 chains. Longest chain 16 peptides. Score 0.448 Round 5: 721 peptides, 114 chains. Longest chain 16 peptides. Score 0.431 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 114, Residues 624, Estimated correctness of the model 38.6 % 3 chains (19 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2awa-2_warpNtrace.pdb as input Building loops using Loopy2018 114 chains (624 residues) following loop building 3 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 48746 reflections ( 97.20 % complete ) and 23764 restraints for refining 11585 atoms. 21325 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2355 (Rfree = 0.000) for 11585 atoms. Found 0 (170 requested) and removed 85 (85 requested) atoms. Cycle 47: After refmac, R = 0.2017 (Rfree = 0.000) for 11486 atoms. Found 0 (169 requested) and removed 84 (84 requested) atoms. Cycle 48: After refmac, R = 0.1914 (Rfree = 0.000) for 11392 atoms. Found 0 (167 requested) and removed 80 (83 requested) atoms. Cycle 49: After refmac, R = 0.1893 (Rfree = 0.000) for 11307 atoms. TimeTaking 133.95