null Mon 24 Dec 07:48:32 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 1vp7-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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/1vp7-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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 07:48:37 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/1vp7-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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 570 and 0 Target number of residues in the AU: 570 Target solvent content: 0.5492 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.4-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.60 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: 207.138 3.401 Wilson plot Bfac: 35.36 10256 reflections ( 99.67 % complete ) and 0 restraints for refining 5305 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3184 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3230 (Rfree = 0.000) for 5305 atoms. Found 40 (40 requested) and removed 54 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.94 2.82 Search for helices and strands: 0 residues in 0 chains, 5389 seeds are put forward NCS extension: 0 residues added, 5389 seeds are put forward Round 1: 204 peptides, 37 chains. Longest chain 14 peptides. Score 0.329 Round 2: 282 peptides, 41 chains. Longest chain 23 peptides. Score 0.473 Round 3: 304 peptides, 39 chains. Longest chain 21 peptides. Score 0.537 Round 4: 292 peptides, 38 chains. Longest chain 23 peptides. Score 0.522 Round 5: 312 peptides, 42 chains. Longest chain 19 peptides. Score 0.526 Taking the results from Round 3 Chains 41, Residues 265, Estimated correctness of the model 6.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8753 restraints for refining 4090 atoms. 7669 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3016 (Rfree = 0.000) for 4090 atoms. Found 30 (30 requested) and removed 40 (15 requested) atoms. Cycle 2: After refmac, R = 0.3014 (Rfree = 0.000) for 3950 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 3: After refmac, R = 0.3019 (Rfree = 0.000) for 3882 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 4: After refmac, R = 0.2987 (Rfree = 0.000) for 3848 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 5: After refmac, R = 0.2696 (Rfree = 0.000) for 3800 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.76 2.65 Search for helices and strands: 0 residues in 0 chains, 3988 seeds are put forward NCS extension: 6 residues added (3 deleted due to clashes), 3994 seeds are put forward Round 1: 264 peptides, 48 chains. Longest chain 10 peptides. Score 0.361 Round 2: 298 peptides, 43 chains. Longest chain 15 peptides. Score 0.488 Round 3: 308 peptides, 45 chains. Longest chain 21 peptides. Score 0.491 Round 4: 311 peptides, 39 chains. Longest chain 33 peptides. Score 0.551 Round 5: 308 peptides, 38 chains. Longest chain 28 peptides. Score 0.554 Taking the results from Round 5 Chains 38, Residues 270, Estimated correctness of the model 12.9 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7684 restraints for refining 3796 atoms. 6487 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3051 (Rfree = 0.000) for 3796 atoms. Found 28 (28 requested) and removed 36 (14 requested) atoms. Cycle 7: After refmac, R = 0.3076 (Rfree = 0.000) for 3725 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 8: After refmac, R = 0.2667 (Rfree = 0.000) for 3690 atoms. Found 24 (28 requested) and removed 19 (14 requested) atoms. Cycle 9: After refmac, R = 0.2704 (Rfree = 0.000) for 3667 atoms. Found 19 (27 requested) and removed 20 (13 requested) atoms. Cycle 10: After refmac, R = 0.2553 (Rfree = 0.000) for 3644 atoms. Found 21 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.73 2.62 Search for helices and strands: 0 residues in 0 chains, 3768 seeds are put forward NCS extension: 0 residues added, 3768 seeds are put forward Round 1: 279 peptides, 46 chains. Longest chain 31 peptides. Score 0.417 Round 2: 319 peptides, 44 chains. Longest chain 17 peptides. Score 0.522 Round 3: 336 peptides, 40 chains. Longest chain 32 peptides. Score 0.589 Round 4: 335 peptides, 43 chains. Longest chain 27 peptides. Score 0.562 Round 5: 340 peptides, 44 chains. Longest chain 27 peptides. Score 0.563 Taking the results from Round 3 Chains 43, Residues 296, Estimated correctness of the model 25.0 % 3 chains (61 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7046 restraints for refining 3727 atoms. 5671 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3179 (Rfree = 0.000) for 3727 atoms. Found 28 (28 requested) and removed 48 (14 requested) atoms. Cycle 12: After refmac, R = 0.2951 (Rfree = 0.000) for 3669 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 13: After refmac, R = 0.2886 (Rfree = 0.000) for 3636 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 14: After refmac, R = 0.2795 (Rfree = 0.000) for 3619 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 15: After refmac, R = 0.2776 (Rfree = 0.000) for 3601 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.77 2.66 Search for helices and strands: 0 residues in 0 chains, 3759 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3776 seeds are put forward Round 1: 290 peptides, 45 chains. Longest chain 20 peptides. Score 0.452 Round 2: 319 peptides, 44 chains. Longest chain 24 peptides. Score 0.522 Round 3: 321 peptides, 45 chains. Longest chain 23 peptides. Score 0.518 Round 4: 327 peptides, 47 chains. Longest chain 23 peptides. Score 0.512 Round 5: 329 peptides, 42 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 5 Chains 44, Residues 287, Estimated correctness of the model 15.0 % 3 chains (53 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7709 restraints for refining 3872 atoms. 6394 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2866 (Rfree = 0.000) for 3872 atoms. Found 28 (29 requested) and removed 34 (14 requested) atoms. Cycle 17: After refmac, R = 0.2774 (Rfree = 0.000) for 3821 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 18: After refmac, R = 0.2583 (Rfree = 0.000) for 3801 atoms. Found 21 (28 requested) and removed 18 (14 requested) atoms. Cycle 19: After refmac, R = 0.2748 (Rfree = 0.000) for 3775 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 20: After refmac, R = 0.2614 (Rfree = 0.000) for 3749 atoms. Found 23 (28 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.77 2.66 Search for helices and strands: 0 residues in 0 chains, 3915 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 3928 seeds are put forward Round 1: 281 peptides, 46 chains. Longest chain 22 peptides. Score 0.421 Round 2: 326 peptides, 44 chains. Longest chain 29 peptides. Score 0.536 Round 3: 329 peptides, 44 chains. Longest chain 25 peptides. Score 0.542 Round 4: 317 peptides, 46 chains. Longest chain 19 peptides. Score 0.500 Round 5: 312 peptides, 41 chains. Longest chain 17 peptides. Score 0.535 Taking the results from Round 3 Chains 48, Residues 285, Estimated correctness of the model 8.5 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7806 restraints for refining 3813 atoms. 6537 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2936 (Rfree = 0.000) for 3813 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 22: After refmac, R = 0.2960 (Rfree = 0.000) for 3781 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 23: After refmac, R = 0.2695 (Rfree = 0.000) for 3766 atoms. Found 19 (28 requested) and removed 21 (14 requested) atoms. Cycle 24: After refmac, R = 0.2677 (Rfree = 0.000) for 3749 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 25: After refmac, R = 0.2530 (Rfree = 0.000) for 3747 atoms. Found 22 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.82 2.71 Search for helices and strands: 0 residues in 0 chains, 3937 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 3974 seeds are put forward Round 1: 303 peptides, 46 chains. Longest chain 20 peptides. Score 0.471 Round 2: 306 peptides, 43 chains. Longest chain 21 peptides. Score 0.505 Round 3: 305 peptides, 39 chains. Longest chain 28 peptides. Score 0.539 Round 4: 309 peptides, 39 chains. Longest chain 30 peptides. Score 0.547 Round 5: 317 peptides, 46 chains. Longest chain 28 peptides. Score 0.500 Taking the results from Round 4 Chains 41, Residues 270, Estimated correctness of the model 10.4 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8229 restraints for refining 3900 atoms. 7082 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2835 (Rfree = 0.000) for 3900 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. Cycle 27: After refmac, R = 0.2718 (Rfree = 0.000) for 3867 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 28: After refmac, R = 0.2684 (Rfree = 0.000) for 3849 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 29: After refmac, R = 0.2565 (Rfree = 0.000) for 3849 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 30: After refmac, R = 0.2583 (Rfree = 0.000) for 3843 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.73 2.62 Search for helices and strands: 0 residues in 0 chains, 4033 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 4052 seeds are put forward Round 1: 251 peptides, 39 chains. Longest chain 20 peptides. Score 0.423 Round 2: 297 peptides, 38 chains. Longest chain 33 peptides. Score 0.533 Round 3: 304 peptides, 38 chains. Longest chain 28 peptides. Score 0.546 Round 4: 290 peptides, 37 chains. Longest chain 20 peptides. Score 0.528 Round 5: 271 peptides, 35 chains. Longest chain 21 peptides. Score 0.507 Taking the results from Round 3 Chains 39, Residues 266, Estimated correctness of the model 10.0 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8222 restraints for refining 3960 atoms. 7052 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2846 (Rfree = 0.000) for 3960 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. Cycle 32: After refmac, R = 0.2810 (Rfree = 0.000) for 3926 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 33: After refmac, R = 0.2644 (Rfree = 0.000) for 3914 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 34: After refmac, R = 0.2694 (Rfree = 0.000) for 3900 atoms. Found 27 (29 requested) and removed 27 (14 requested) atoms. Cycle 35: After refmac, R = 0.2565 (Rfree = 0.000) for 3891 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.80 2.69 Search for helices and strands: 0 residues in 0 chains, 4061 seeds are put forward NCS extension: 0 residues added, 4061 seeds are put forward Round 1: 252 peptides, 43 chains. Longest chain 13 peptides. Score 0.384 Round 2: 286 peptides, 45 chains. Longest chain 22 peptides. Score 0.443 Round 3: 288 peptides, 44 chains. Longest chain 15 peptides. Score 0.457 Round 4: 298 peptides, 42 chains. Longest chain 15 peptides. Score 0.498 Round 5: 296 peptides, 43 chains. Longest chain 22 peptides. Score 0.484 Taking the results from Round 4 Chains 42, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8539 restraints for refining 3917 atoms. 7557 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2867 (Rfree = 0.000) for 3917 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 37: After refmac, R = 0.2811 (Rfree = 0.000) for 3901 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 38: After refmac, R = 0.2642 (Rfree = 0.000) for 3891 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. Cycle 39: After refmac, R = 0.2646 (Rfree = 0.000) for 3893 atoms. Found 24 (29 requested) and removed 19 (14 requested) atoms. Cycle 40: After refmac, R = 0.2540 (Rfree = 0.000) for 3887 atoms. Found 18 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.82 2.71 Search for helices and strands: 0 residues in 0 chains, 4020 seeds are put forward NCS extension: 2 residues added (4 deleted due to clashes), 4022 seeds are put forward Round 1: 242 peptides, 42 chains. Longest chain 20 peptides. Score 0.370 Round 2: 279 peptides, 40 chains. Longest chain 25 peptides. Score 0.476 Round 3: 285 peptides, 41 chains. Longest chain 20 peptides. Score 0.479 Round 4: 281 peptides, 34 chains. Longest chain 39 peptides. Score 0.537 Round 5: 286 peptides, 42 chains. Longest chain 23 peptides. Score 0.472 Taking the results from Round 4 Chains 36, Residues 247, Estimated correctness of the model 6.7 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8669 restraints for refining 3957 atoms. 7668 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2876 (Rfree = 0.000) for 3957 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 42: After refmac, R = 0.2663 (Rfree = 0.000) for 3949 atoms. Found 28 (29 requested) and removed 20 (14 requested) atoms. Cycle 43: After refmac, R = 0.2538 (Rfree = 0.000) for 3948 atoms. Found 16 (29 requested) and removed 17 (14 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 3941 atoms. Found 15 (29 requested) and removed 18 (14 requested) atoms. Cycle 45: After refmac, R = 0.2478 (Rfree = 0.000) for 3936 atoms. Found 9 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.82 2.71 Search for helices and strands: 0 residues in 0 chains, 4053 seeds are put forward NCS extension: 5 residues added (3 deleted due to clashes), 4058 seeds are put forward Round 1: 246 peptides, 43 chains. Longest chain 22 peptides. Score 0.369 Round 2: 278 peptides, 45 chains. Longest chain 17 peptides. Score 0.425 Round 3: 264 peptides, 39 chains. Longest chain 19 peptides. Score 0.453 Round 4: 263 peptides, 40 chains. Longest chain 17 peptides. Score 0.441 Round 5: 263 peptides, 35 chains. Longest chain 30 peptides. Score 0.490 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 228, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (228 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10256 reflections ( 99.67 % complete ) and 9054 restraints for refining 4121 atoms. 8104 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2689 (Rfree = 0.000) for 4121 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2518 (Rfree = 0.000) for 4093 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2461 (Rfree = 0.000) for 4073 atoms. Found 0 (30 requested) and removed 11 (15 requested) atoms. Cycle 49: After refmac, R = 0.2430 (Rfree = 0.000) for 4060 atoms. Found 0 (30 requested) and removed 9 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:50:10 GMT 2018 Job finished. TimeTaking 61.63 Used memory is bytes: 14111032