Mon 24 Dec 07:56:52 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 2op5-2.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2op5-2.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2op5-2.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-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/2op5-2.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-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 07:56:56 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/2op5-2.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-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 637 and 0 Target number of residues in the AU: 637 Target solvent content: 0.5032 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-2.2-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: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-2.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.55 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 1 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: 73.087 2.190 Wilson plot Bfac: 24.02 36536 reflections ( 99.76 % complete ) and 0 restraints for refining 6194 atoms. Observations/parameters ratio is 1.47 ------------------------------------------------------ Starting model: R = 0.3455 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2978 (Rfree = 0.000) for 6194 atoms. Found 106 (163 requested) and removed 101 (81 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.19 2.34 NCS extension: 0 residues added, 6199 seeds are put forward Round 1: 343 peptides, 64 chains. Longest chain 14 peptides. Score 0.385 Round 2: 400 peptides, 52 chains. Longest chain 16 peptides. Score 0.602 Round 3: 419 peptides, 55 chains. Longest chain 17 peptides. Score 0.612 Round 4: 443 peptides, 50 chains. Longest chain 28 peptides. Score 0.683 Round 5: 453 peptides, 46 chains. Longest chain 24 peptides. Score 0.721 Taking the results from Round 5 Chains 47, Residues 407, Estimated correctness of the model 90.8 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 10942 restraints for refining 5365 atoms. 9295 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3295 (Rfree = 0.000) for 5365 atoms. Found 84 (141 requested) and removed 81 (70 requested) atoms. Cycle 2: After refmac, R = 0.3072 (Rfree = 0.000) for 5360 atoms. Found 67 (138 requested) and removed 74 (70 requested) atoms. Cycle 3: After refmac, R = 0.2919 (Rfree = 0.000) for 5340 atoms. Found 78 (135 requested) and removed 71 (70 requested) atoms. Cycle 4: After refmac, R = 0.2852 (Rfree = 0.000) for 5336 atoms. Found 62 (133 requested) and removed 66 (70 requested) atoms. Cycle 5: After refmac, R = 0.2759 (Rfree = 0.000) for 5331 atoms. Found 61 (130 requested) and removed 42 (70 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.14 2.29 NCS extension: 16 residues added (5 deleted due to clashes), 5402 seeds are put forward Round 1: 457 peptides, 48 chains. Longest chain 26 peptides. Score 0.714 Round 2: 475 peptides, 41 chains. Longest chain 42 peptides. Score 0.773 Round 3: 483 peptides, 42 chains. Longest chain 30 peptides. Score 0.776 Round 4: 472 peptides, 38 chains. Longest chain 37 peptides. Score 0.785 Round 5: 479 peptides, 38 chains. Longest chain 51 peptides. Score 0.792 Taking the results from Round 5 Chains 40, Residues 441, Estimated correctness of the model 94.6 % 3 chains (91 residues) have been docked in sequence Building loops using Loopy2018 40 chains (441 residues) following loop building 3 chains (91 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 9911 restraints for refining 5365 atoms. 7795 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3020 (Rfree = 0.000) for 5365 atoms. Found 114 (127 requested) and removed 79 (70 requested) atoms. Cycle 7: After refmac, R = 0.2846 (Rfree = 0.000) for 5398 atoms. Found 68 (125 requested) and removed 52 (71 requested) atoms. Cycle 8: After refmac, R = 0.2725 (Rfree = 0.000) for 5410 atoms. Found 63 (123 requested) and removed 33 (71 requested) atoms. Cycle 9: After refmac, R = 0.2647 (Rfree = 0.000) for 5437 atoms. Found 49 (120 requested) and removed 24 (71 requested) atoms. Cycle 10: After refmac, R = 0.2604 (Rfree = 0.000) for 5460 atoms. Found 43 (121 requested) and removed 23 (72 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.13 2.28 NCS extension: 14 residues added (1 deleted due to clashes), 5505 seeds are put forward Round 1: 463 peptides, 42 chains. Longest chain 36 peptides. Score 0.755 Round 2: 490 peptides, 35 chains. Longest chain 51 peptides. Score 0.816 Round 3: 496 peptides, 40 chains. Longest chain 42 peptides. Score 0.799 Round 4: 500 peptides, 38 chains. Longest chain 51 peptides. Score 0.811 Round 5: 494 peptides, 43 chains. Longest chain 30 peptides. Score 0.783 Taking the results from Round 2 Chains 38, Residues 455, Estimated correctness of the model 95.7 % 6 chains (155 residues) have been docked in sequence Building loops using Loopy2018 38 chains (455 residues) following loop building 6 chains (155 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 9107 restraints for refining 5465 atoms. 6627 conditional restraints added. Observations/parameters ratio is 1.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2849 (Rfree = 0.000) for 5465 atoms. Found 118 (118 requested) and removed 87 (72 requested) atoms. Cycle 12: After refmac, R = 0.2726 (Rfree = 0.000) for 5494 atoms. Found 64 (116 requested) and removed 66 (72 requested) atoms. Cycle 13: After refmac, R = 0.2644 (Rfree = 0.000) for 5489 atoms. Found 55 (113 requested) and removed 24 (72 requested) atoms. Cycle 14: After refmac, R = 0.2585 (Rfree = 0.000) for 5518 atoms. Found 47 (114 requested) and removed 19 (73 requested) atoms. Cycle 15: After refmac, R = 0.2544 (Rfree = 0.000) for 5541 atoms. Found 49 (114 requested) and removed 20 (73 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.12 2.27 NCS extension: 23 residues added (10 deleted due to clashes), 5602 seeds are put forward Round 1: 489 peptides, 40 chains. Longest chain 36 peptides. Score 0.792 Round 2: 495 peptides, 40 chains. Longest chain 57 peptides. Score 0.798 Round 3: 504 peptides, 39 chains. Longest chain 54 peptides. Score 0.810 Round 4: 498 peptides, 44 chains. Longest chain 30 peptides. Score 0.782 Round 5: 500 peptides, 38 chains. Longest chain 66 peptides. Score 0.811 Taking the results from Round 5 Chains 39, Residues 462, Estimated correctness of the model 95.5 % 5 chains (172 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 63 A 38 chains (467 residues) following loop building 4 chains (177 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 8822 restraints for refining 5533 atoms. 6185 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2887 (Rfree = 0.000) for 5533 atoms. Found 114 (114 requested) and removed 87 (73 requested) atoms. Cycle 17: After refmac, R = 0.2754 (Rfree = 0.000) for 5556 atoms. Found 76 (112 requested) and removed 63 (73 requested) atoms. Cycle 18: After refmac, R = 0.2670 (Rfree = 0.000) for 5566 atoms. Found 77 (109 requested) and removed 18 (73 requested) atoms. Cycle 19: After refmac, R = 0.2618 (Rfree = 0.000) for 5622 atoms. Found 60 (110 requested) and removed 27 (74 requested) atoms. Cycle 20: After refmac, R = 0.2562 (Rfree = 0.000) for 5652 atoms. Found 39 (110 requested) and removed 30 (74 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.12 2.27 NCS extension: 12 residues added (16 deleted due to clashes), 5682 seeds are put forward Round 1: 487 peptides, 38 chains. Longest chain 38 peptides. Score 0.800 Round 2: 500 peptides, 40 chains. Longest chain 56 peptides. Score 0.802 Round 3: 507 peptides, 37 chains. Longest chain 50 peptides. Score 0.821 Round 4: 508 peptides, 35 chains. Longest chain 86 peptides. Score 0.831 Round 5: 502 peptides, 40 chains. Longest chain 54 peptides. Score 0.804 Taking the results from Round 4 Chains 38, Residues 473, Estimated correctness of the model 96.3 % 5 chains (181 residues) have been docked in sequence Building loops using Loopy2018 38 chains (473 residues) following loop building 5 chains (181 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 8849 restraints for refining 5617 atoms. 6168 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2783 (Rfree = 0.000) for 5617 atoms. Found 107 (107 requested) and removed 86 (74 requested) atoms. Cycle 22: After refmac, R = 0.2662 (Rfree = 0.000) for 5637 atoms. Found 82 (104 requested) and removed 48 (74 requested) atoms. Cycle 23: After refmac, R = 0.2573 (Rfree = 0.000) for 5670 atoms. Found 85 (101 requested) and removed 30 (74 requested) atoms. Cycle 24: After refmac, R = 0.2533 (Rfree = 0.000) for 5718 atoms. Found 70 (103 requested) and removed 30 (75 requested) atoms. Cycle 25: After refmac, R = 0.2477 (Rfree = 0.000) for 5755 atoms. Found 62 (103 requested) and removed 30 (76 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.12 2.27 NCS extension: 76 residues added (41 deleted due to clashes), 5874 seeds are put forward Round 1: 490 peptides, 34 chains. Longest chain 68 peptides. Score 0.820 Round 2: 505 peptides, 33 chains. Longest chain 85 peptides. Score 0.836 Round 3: 500 peptides, 36 chains. Longest chain 43 peptides. Score 0.820 Round 4: 499 peptides, 35 chains. Longest chain 43 peptides. Score 0.823 Round 5: 483 peptides, 37 chains. Longest chain 41 peptides. Score 0.801 Taking the results from Round 2 Chains 33, Residues 472, Estimated correctness of the model 96.5 % 4 chains (171 residues) have been docked in sequence Building loops using Loopy2018 33 chains (472 residues) following loop building 4 chains (171 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 8941 restraints for refining 5667 atoms. 6314 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2645 (Rfree = 0.000) for 5667 atoms. Found 101 (101 requested) and removed 81 (74 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 5684 atoms. Found 87 (99 requested) and removed 33 (75 requested) atoms. Cycle 28: After refmac, R = 0.2487 (Rfree = 0.000) for 5734 atoms. Found 67 (100 requested) and removed 28 (75 requested) atoms. Cycle 29: After refmac, R = 0.2446 (Rfree = 0.000) for 5772 atoms. Found 46 (100 requested) and removed 21 (76 requested) atoms. Cycle 30: After refmac, R = 0.2404 (Rfree = 0.000) for 5796 atoms. Found 38 (101 requested) and removed 15 (76 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.12 2.27 NCS extension: 73 residues added (42 deleted due to clashes), 5895 seeds are put forward Round 1: 486 peptides, 34 chains. Longest chain 54 peptides. Score 0.817 Round 2: 504 peptides, 37 chains. Longest chain 38 peptides. Score 0.819 Round 3: 518 peptides, 34 chains. Longest chain 51 peptides. Score 0.842 Round 4: 511 peptides, 38 chains. Longest chain 51 peptides. Score 0.821 Round 5: 519 peptides, 37 chains. Longest chain 54 peptides. Score 0.831 Taking the results from Round 3 Chains 37, Residues 484, Estimated correctness of the model 96.8 % 6 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 D and 62 D 36 chains (488 residues) following loop building 5 chains (192 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 8726 restraints for refining 5730 atoms. 5946 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2647 (Rfree = 0.000) for 5730 atoms. Found 100 (100 requested) and removed 85 (75 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2529 (Rfree = 0.000) for 5741 atoms. Found 97 (97 requested) and removed 29 (75 requested) atoms. Cycle 33: After refmac, R = 0.2432 (Rfree = 0.000) for 5807 atoms. Found 64 (98 requested) and removed 25 (76 requested) atoms. Cycle 34: After refmac, R = 0.2383 (Rfree = 0.000) for 5842 atoms. Found 76 (99 requested) and removed 21 (77 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2340 (Rfree = 0.000) for 5894 atoms. Found 56 (99 requested) and removed 33 (77 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.11 2.26 NCS extension: 64 residues added (54 deleted due to clashes), 5984 seeds are put forward Round 1: 510 peptides, 37 chains. Longest chain 41 peptides. Score 0.824 Round 2: 521 peptides, 37 chains. Longest chain 34 peptides. Score 0.833 Round 3: 528 peptides, 33 chains. Longest chain 61 peptides. Score 0.853 Round 4: 512 peptides, 42 chains. Longest chain 36 peptides. Score 0.804 Round 5: 498 peptides, 37 chains. Longest chain 54 peptides. Score 0.814 Taking the results from Round 3 Chains 34, Residues 495, Estimated correctness of the model 97.2 % 8 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 28 C and 32 C Built loop between residues 56 D and 62 D 32 chains (503 residues) following loop building 6 chains (253 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 8334 restraints for refining 5901 atoms. 5214 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2649 (Rfree = 0.000) for 5901 atoms. Found 97 (97 requested) and removed 100 (78 requested) atoms. Cycle 37: After refmac, R = 0.2510 (Rfree = 0.000) for 5897 atoms. Found 94 (94 requested) and removed 78 (78 requested) atoms. Cycle 38: After refmac, R = 0.2416 (Rfree = 0.000) for 5912 atoms. Found 90 (90 requested) and removed 41 (78 requested) atoms. Cycle 39: After refmac, R = 0.2357 (Rfree = 0.000) for 5954 atoms. Found 87 (91 requested) and removed 35 (78 requested) atoms. Cycle 40: After refmac, R = 0.2317 (Rfree = 0.000) for 6000 atoms. Found 75 (92 requested) and removed 23 (79 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.10 2.25 NCS extension: 47 residues added (27 deleted due to clashes), 6103 seeds are put forward Round 1: 516 peptides, 35 chains. Longest chain 68 peptides. Score 0.837 Round 2: 521 peptides, 34 chains. Longest chain 39 peptides. Score 0.844 Round 3: 520 peptides, 30 chains. Longest chain 87 peptides. Score 0.859 Round 4: 521 peptides, 36 chains. Longest chain 70 peptides. Score 0.837 Round 5: 514 peptides, 31 chains. Longest chain 54 peptides. Score 0.851 Taking the results from Round 3 Chains 32, Residues 490, Estimated correctness of the model 97.4 % 6 chains (221 residues) have been docked in sequence Building loops using Loopy2018 32 chains (490 residues) following loop building 6 chains (221 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 8591 restraints for refining 5928 atoms. 5662 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2520 (Rfree = 0.000) for 5928 atoms. Found 90 (90 requested) and removed 84 (78 requested) atoms. Cycle 42: After refmac, R = 0.2417 (Rfree = 0.000) for 5934 atoms. Found 87 (87 requested) and removed 44 (78 requested) atoms. Cycle 43: After refmac, R = 0.2340 (Rfree = 0.000) for 5975 atoms. Found 82 (85 requested) and removed 25 (79 requested) atoms. Cycle 44: After refmac, R = 0.2275 (Rfree = 0.000) for 6030 atoms. Found 68 (86 requested) and removed 30 (79 requested) atoms. Cycle 45: After refmac, R = 0.2246 (Rfree = 0.000) for 6065 atoms. Found 77 (86 requested) and removed 35 (80 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.10 2.25 NCS extension: 46 residues added (51 deleted due to clashes), 6159 seeds are put forward Round 1: 497 peptides, 35 chains. Longest chain 51 peptides. Score 0.822 Round 2: 510 peptides, 33 chains. Longest chain 51 peptides. Score 0.840 Round 3: 502 peptides, 36 chains. Longest chain 35 peptides. Score 0.822 Round 4: 496 peptides, 36 chains. Longest chain 40 peptides. Score 0.817 Round 5: 501 peptides, 36 chains. Longest chain 54 peptides. Score 0.821 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 477, Estimated correctness of the model 96.7 % 8 chains (225 residues) have been docked in sequence Sequence coverage is 47 % Consider running further cycles of model building using 2op5-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 18 B and 21 B Built loop between residues 57 D and 62 D 31 chains (483 residues) following loop building 6 chains (231 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 36536 reflections ( 99.76 % complete ) and 8745 restraints for refining 6008 atoms. 5799 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2462 (Rfree = 0.000) for 6008 atoms. Found 0 (85 requested) and removed 15 (79 requested) atoms. Cycle 47: After refmac, R = 0.2373 (Rfree = 0.000) for 5992 atoms. Found 0 (82 requested) and removed 6 (79 requested) atoms. Cycle 48: After refmac, R = 0.2331 (Rfree = 0.000) for 5986 atoms. Found 0 (79 requested) and removed 5 (79 requested) atoms. Cycle 49: After refmac, R = 0.2317 (Rfree = 0.000) for 5981 atoms. Found 0 (79 requested) and removed 4 (79 requested) atoms. Writing output files ... TimeTaking 60.53