null Tue 25 Dec 19:27:57 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 1vp7-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.8-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/1vp7-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.8-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 19:28:12 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/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.8-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 509 and 0 Target number of residues in the AU: 509 Target solvent content: 0.5975 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: 1vp7-3.8-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.8-parrot-hancs.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 3.800 Wilson plot Bfac: 51.38 7444 reflections ( 99.55 % complete ) and 0 restraints for refining 5282 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3196 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3369 (Rfree = 0.000) for 5282 atoms. Found 29 (29 requested) and removed 45 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.18 Search for helices and strands: 0 residues in 0 chains, 5372 seeds are put forward NCS extension: 0 residues added, 5372 seeds are put forward Round 1: 191 peptides, 39 chains. Longest chain 8 peptides. Score 0.270 Round 2: 253 peptides, 40 chains. Longest chain 13 peptides. Score 0.418 Round 3: 246 peptides, 36 chains. Longest chain 13 peptides. Score 0.443 Round 4: 253 peptides, 35 chains. Longest chain 16 peptides. Score 0.468 Round 5: 253 peptides, 33 chains. Longest chain 24 peptides. Score 0.488 Taking the results from Round 5 Chains 33, Residues 220, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 9524 restraints for refining 4016 atoms. 8641 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2951 (Rfree = 0.000) for 4016 atoms. Found 22 (22 requested) and removed 46 (11 requested) atoms. Cycle 2: After refmac, R = 0.2842 (Rfree = 0.000) for 3856 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 3: After refmac, R = 0.2687 (Rfree = 0.000) for 3799 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 4: After refmac, R = 0.2377 (Rfree = 0.000) for 3750 atoms. Found 7 (20 requested) and removed 16 (10 requested) atoms. Cycle 5: After refmac, R = 0.2193 (Rfree = 0.000) for 3705 atoms. Found 11 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 3900 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3924 seeds are put forward Round 1: 220 peptides, 37 chains. Longest chain 12 peptides. Score 0.370 Round 2: 240 peptides, 36 chains. Longest chain 12 peptides. Score 0.429 Round 3: 252 peptides, 33 chains. Longest chain 14 peptides. Score 0.486 Round 4: 262 peptides, 34 chains. Longest chain 14 peptides. Score 0.498 Round 5: 248 peptides, 32 chains. Longest chain 15 peptides. Score 0.488 Taking the results from Round 4 Chains 34, Residues 228, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 7851 restraints for refining 3622 atoms. 6937 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2914 (Rfree = 0.000) for 3622 atoms. Found 19 (19 requested) and removed 55 (9 requested) atoms. Cycle 7: After refmac, R = 0.2731 (Rfree = 0.000) for 3526 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 8: After refmac, R = 0.2806 (Rfree = 0.000) for 3485 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 9: After refmac, R = 0.2430 (Rfree = 0.000) for 3446 atoms. Found 17 (19 requested) and removed 24 (9 requested) atoms. Cycle 10: After refmac, R = 0.2334 (Rfree = 0.000) for 3429 atoms. Found 15 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 3594 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3609 seeds are put forward Round 1: 226 peptides, 37 chains. Longest chain 12 peptides. Score 0.385 Round 2: 264 peptides, 35 chains. Longest chain 17 peptides. Score 0.492 Round 3: 246 peptides, 34 chains. Longest chain 20 peptides. Score 0.463 Round 4: 257 peptides, 34 chains. Longest chain 17 peptides. Score 0.487 Round 5: 241 peptides, 32 chains. Longest chain 16 peptides. Score 0.472 Taking the results from Round 2 Chains 35, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 7295 restraints for refining 3433 atoms. 6414 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2685 (Rfree = 0.000) for 3433 atoms. Found 18 (18 requested) and removed 30 (9 requested) atoms. Cycle 12: After refmac, R = 0.2465 (Rfree = 0.000) for 3396 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 13: After refmac, R = 0.2428 (Rfree = 0.000) for 3380 atoms. Found 17 (18 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.2023 (Rfree = 0.000) for 3362 atoms. Found 12 (18 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.2054 (Rfree = 0.000) for 3350 atoms. Found 11 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 3514 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3534 seeds are put forward Round 1: 229 peptides, 41 chains. Longest chain 11 peptides. Score 0.348 Round 2: 252 peptides, 41 chains. Longest chain 14 peptides. Score 0.405 Round 3: 251 peptides, 39 chains. Longest chain 15 peptides. Score 0.423 Round 4: 244 peptides, 35 chains. Longest chain 18 peptides. Score 0.448 Round 5: 268 peptides, 37 chains. Longest chain 19 peptides. Score 0.482 Taking the results from Round 5 Chains 37, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8061 restraints for refining 3655 atoms. 7174 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2697 (Rfree = 0.000) for 3655 atoms. Found 20 (20 requested) and removed 43 (10 requested) atoms. Cycle 17: After refmac, R = 0.2401 (Rfree = 0.000) for 3605 atoms. Found 17 (19 requested) and removed 26 (9 requested) atoms. Cycle 18: After refmac, R = 0.2378 (Rfree = 0.000) for 3577 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 19: After refmac, R = 0.2421 (Rfree = 0.000) for 3554 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 20: After refmac, R = 0.2252 (Rfree = 0.000) for 3537 atoms. Found 10 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 3733 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3760 seeds are put forward Round 1: 234 peptides, 43 chains. Longest chain 16 peptides. Score 0.339 Round 2: 267 peptides, 45 chains. Longest chain 14 peptides. Score 0.399 Round 3: 250 peptides, 41 chains. Longest chain 14 peptides. Score 0.400 Round 4: 259 peptides, 36 chains. Longest chain 17 peptides. Score 0.472 Round 5: 255 peptides, 42 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 4 Chains 36, Residues 223, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 7934 restraints for refining 3699 atoms. 7015 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2876 (Rfree = 0.000) for 3699 atoms. Found 20 (20 requested) and removed 53 (10 requested) atoms. Cycle 22: After refmac, R = 0.2631 (Rfree = 0.000) for 3636 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 23: After refmac, R = 0.2282 (Rfree = 0.000) for 3602 atoms. Found 12 (19 requested) and removed 18 (9 requested) atoms. Cycle 24: After refmac, R = 0.2269 (Rfree = 0.000) for 3579 atoms. Found 12 (19 requested) and removed 15 (9 requested) atoms. Cycle 25: After refmac, R = 0.2566 (Rfree = 0.000) for 3571 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 3767 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3785 seeds are put forward Round 1: 214 peptides, 40 chains. Longest chain 9 peptides. Score 0.321 Round 2: 256 peptides, 44 chains. Longest chain 15 peptides. Score 0.383 Round 3: 243 peptides, 40 chains. Longest chain 11 peptides. Score 0.394 Round 4: 251 peptides, 40 chains. Longest chain 14 peptides. Score 0.413 Round 5: 245 peptides, 36 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 5 Chains 36, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8601 restraints for refining 3781 atoms. 7801 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3187 (Rfree = 0.000) for 3781 atoms. Found 20 (20 requested) and removed 49 (10 requested) atoms. Cycle 27: After refmac, R = 0.2768 (Rfree = 0.000) for 3723 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 28: After refmac, R = 0.2638 (Rfree = 0.000) for 3691 atoms. Found 20 (20 requested) and removed 35 (10 requested) atoms. Cycle 29: After refmac, R = 0.2558 (Rfree = 0.000) for 3661 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 30: After refmac, R = 0.2463 (Rfree = 0.000) for 3648 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 3799 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3817 seeds are put forward Round 1: 208 peptides, 46 chains. Longest chain 9 peptides. Score 0.236 Round 2: 242 peptides, 44 chains. Longest chain 11 peptides. Score 0.349 Round 3: 248 peptides, 42 chains. Longest chain 12 peptides. Score 0.385 Round 4: 248 peptides, 42 chains. Longest chain 11 peptides. Score 0.385 Round 5: 231 peptides, 38 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 5 Chains 38, Residues 193, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8528 restraints for refining 3786 atoms. 7758 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2889 (Rfree = 0.000) for 3786 atoms. Found 20 (20 requested) and removed 51 (10 requested) atoms. Cycle 32: After refmac, R = 0.2476 (Rfree = 0.000) for 3714 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 33: After refmac, R = 0.2373 (Rfree = 0.000) for 3687 atoms. Found 20 (20 requested) and removed 32 (10 requested) atoms. Cycle 34: After refmac, R = 0.2290 (Rfree = 0.000) for 3663 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 35: After refmac, R = 0.2285 (Rfree = 0.000) for 3657 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.04 Search for helices and strands: 0 residues in 0 chains, 3793 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3805 seeds are put forward Round 1: 205 peptides, 43 chains. Longest chain 8 peptides. Score 0.262 Round 2: 235 peptides, 40 chains. Longest chain 13 peptides. Score 0.374 Round 3: 222 peptides, 36 chains. Longest chain 15 peptides. Score 0.386 Round 4: 218 peptides, 39 chains. Longest chain 10 peptides. Score 0.342 Round 5: 232 peptides, 38 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 5 Chains 38, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8800 restraints for refining 3829 atoms. 8062 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2649 (Rfree = 0.000) for 3829 atoms. Found 21 (21 requested) and removed 37 (10 requested) atoms. Cycle 37: After refmac, R = 0.2546 (Rfree = 0.000) for 3779 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 38: After refmac, R = 0.2450 (Rfree = 0.000) for 3758 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 39: After refmac, R = 0.2536 (Rfree = 0.000) for 3750 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 40: After refmac, R = 0.2111 (Rfree = 0.000) for 3732 atoms. Found 15 (20 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 3887 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3901 seeds are put forward Round 1: 171 peptides, 36 chains. Longest chain 11 peptides. Score 0.249 Round 2: 201 peptides, 38 chains. Longest chain 10 peptides. Score 0.309 Round 3: 204 peptides, 36 chains. Longest chain 11 peptides. Score 0.340 Round 4: 207 peptides, 34 chains. Longest chain 11 peptides. Score 0.370 Round 5: 220 peptides, 36 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 5 Chains 36, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.55 % complete ) and 8548 restraints for refining 3755 atoms. 7848 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3122 (Rfree = 0.000) for 3755 atoms. Found 20 (20 requested) and removed 44 (10 requested) atoms. Cycle 42: After refmac, R = 0.2731 (Rfree = 0.000) for 3712 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 43: After refmac, R = 0.2696 (Rfree = 0.000) for 3683 atoms. Found 20 (20 requested) and removed 37 (10 requested) atoms. Cycle 44: After refmac, R = 0.2741 (Rfree = 0.000) for 3657 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 45: After refmac, R = 0.2771 (Rfree = 0.000) for 3642 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.20 Search for helices and strands: 0 residues in 0 chains, 3802 seeds are put forward NCS extension: 0 residues added, 3802 seeds are put forward Round 1: 170 peptides, 34 chains. Longest chain 10 peptides. Score 0.271 Round 2: 191 peptides, 37 chains. Longest chain 11 peptides. Score 0.294 Round 3: 202 peptides, 34 chains. Longest chain 11 peptides. Score 0.358 Round 4: 213 peptides, 37 chains. Longest chain 14 peptides. Score 0.352 Round 5: 202 peptides, 30 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 172, 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 1vp7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7444 reflections ( 99.55 % complete ) and 8842 restraints for refining 3807 atoms. 8184 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3209 (Rfree = 0.000) for 3807 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2944 (Rfree = 0.000) for 3778 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2868 (Rfree = 0.000) for 3755 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2382 (Rfree = 0.000) for 3732 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:06:57 GMT 2018 Job finished. TimeTaking 98.99 Used memory is bytes: 14757304