Mon 24 Dec 07:56:09 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 1vp7-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp7-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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/1vp7-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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 07:56:13 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/1vp7-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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 595 and 0 Target number of residues in the AU: 595 Target solvent content: 0.5294 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: 1vp7-3.2-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.2-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 3.200 Wilson plot Bfac: 30.03 12229 reflections ( 99.72 % complete ) and 0 restraints for refining 5307 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3188 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3005 (Rfree = 0.000) for 5307 atoms. Found 47 (47 requested) and removed 69 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.68 2.57 Search for helices and strands: 0 residues in 0 chains, 5387 seeds are put forward NCS extension: 0 residues added, 5387 seeds are put forward Round 1: 251 peptides, 38 chains. Longest chain 17 peptides. Score 0.433 Round 2: 301 peptides, 38 chains. Longest chain 19 peptides. Score 0.541 Round 3: 318 peptides, 40 chains. Longest chain 18 peptides. Score 0.556 Round 4: 331 peptides, 38 chains. Longest chain 18 peptides. Score 0.597 Round 5: 342 peptides, 38 chains. Longest chain 24 peptides. Score 0.616 Taking the results from Round 5 Chains 38, Residues 304, Estimated correctness of the model 45.3 % 5 chains (77 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 8100 restraints for refining 4229 atoms. 6616 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2917 (Rfree = 0.000) for 4229 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 2: After refmac, R = 0.2860 (Rfree = 0.000) for 4102 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 3: After refmac, R = 0.2780 (Rfree = 0.000) for 4060 atoms. Found 32 (36 requested) and removed 28 (18 requested) atoms. Cycle 4: After refmac, R = 0.2667 (Rfree = 0.000) for 4040 atoms. Found 27 (36 requested) and removed 24 (18 requested) atoms. Cycle 5: After refmac, R = 0.2609 (Rfree = 0.000) for 4030 atoms. Found 16 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.65 2.55 Search for helices and strands: 0 residues in 0 chains, 4180 seeds are put forward NCS extension: 4 residues added (1 deleted due to clashes), 4184 seeds are put forward Round 1: 315 peptides, 41 chains. Longest chain 29 peptides. Score 0.541 Round 2: 329 peptides, 39 chains. Longest chain 23 peptides. Score 0.585 Round 3: 334 peptides, 34 chains. Longest chain 31 peptides. Score 0.634 Round 4: 326 peptides, 34 chains. Longest chain 31 peptides. Score 0.621 Round 5: 333 peptides, 35 chains. Longest chain 26 peptides. Score 0.625 Taking the results from Round 3 Chains 34, Residues 300, Estimated correctness of the model 49.9 % 3 chains (62 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 8052 restraints for refining 4083 atoms. 6646 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2906 (Rfree = 0.000) for 4083 atoms. Found 36 (36 requested) and removed 71 (18 requested) atoms. Cycle 7: After refmac, R = 0.2735 (Rfree = 0.000) for 4030 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 8: After refmac, R = 0.2636 (Rfree = 0.000) for 4020 atoms. Found 11 (36 requested) and removed 31 (18 requested) atoms. Cycle 9: After refmac, R = 0.2564 (Rfree = 0.000) for 3992 atoms. Found 12 (35 requested) and removed 20 (17 requested) atoms. Cycle 10: After refmac, R = 0.2591 (Rfree = 0.000) for 3974 atoms. Found 20 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.62 2.52 Search for helices and strands: 0 residues in 0 chains, 4148 seeds are put forward NCS extension: 31 residues added (23 deleted due to clashes), 4179 seeds are put forward Round 1: 312 peptides, 34 chains. Longest chain 38 peptides. Score 0.596 Round 2: 337 peptides, 34 chains. Longest chain 25 peptides. Score 0.639 Round 3: 335 peptides, 33 chains. Longest chain 41 peptides. Score 0.644 Round 4: 351 peptides, 35 chains. Longest chain 32 peptides. Score 0.654 Round 5: 334 peptides, 35 chains. Longest chain 26 peptides. Score 0.626 Taking the results from Round 4 Chains 38, Residues 316, Estimated correctness of the model 54.8 % 4 chains (78 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7791 restraints for refining 4102 atoms. 6257 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2865 (Rfree = 0.000) for 4102 atoms. Found 36 (36 requested) and removed 48 (18 requested) atoms. Cycle 12: After refmac, R = 0.2715 (Rfree = 0.000) for 4061 atoms. Found 23 (36 requested) and removed 34 (18 requested) atoms. Cycle 13: After refmac, R = 0.2619 (Rfree = 0.000) for 4041 atoms. Found 16 (36 requested) and removed 19 (18 requested) atoms. Cycle 14: After refmac, R = 0.2577 (Rfree = 0.000) for 4035 atoms. Found 10 (36 requested) and removed 22 (18 requested) atoms. Cycle 15: After refmac, R = 0.2511 (Rfree = 0.000) for 4018 atoms. Found 9 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.67 2.57 Search for helices and strands: 0 residues in 0 chains, 4148 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 4163 seeds are put forward Round 1: 329 peptides, 40 chains. Longest chain 21 peptides. Score 0.577 Round 2: 340 peptides, 39 chains. Longest chain 22 peptides. Score 0.605 Round 3: 325 peptides, 38 chains. Longest chain 27 peptides. Score 0.586 Round 4: 326 peptides, 36 chains. Longest chain 39 peptides. Score 0.604 Round 5: 350 peptides, 36 chains. Longest chain 26 peptides. Score 0.645 Taking the results from Round 5 Chains 40, Residues 314, Estimated correctness of the model 52.6 % 5 chains (81 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7886 restraints for refining 4125 atoms. 6353 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2902 (Rfree = 0.000) for 4125 atoms. Found 37 (37 requested) and removed 55 (18 requested) atoms. Cycle 17: After refmac, R = 0.2735 (Rfree = 0.000) for 4091 atoms. Found 19 (36 requested) and removed 21 (18 requested) atoms. Cycle 18: After refmac, R = 0.2667 (Rfree = 0.000) for 4079 atoms. Found 16 (36 requested) and removed 19 (18 requested) atoms. Cycle 19: After refmac, R = 0.2621 (Rfree = 0.000) for 4068 atoms. Found 13 (36 requested) and removed 18 (18 requested) atoms. Cycle 20: After refmac, R = 0.2596 (Rfree = 0.000) for 4055 atoms. Found 11 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.72 2.61 Search for helices and strands: 0 residues in 0 chains, 4164 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 4177 seeds are put forward Round 1: 314 peptides, 45 chains. Longest chain 18 peptides. Score 0.503 Round 2: 323 peptides, 40 chains. Longest chain 21 peptides. Score 0.565 Round 3: 335 peptides, 38 chains. Longest chain 28 peptides. Score 0.604 Round 4: 358 peptides, 40 chains. Longest chain 28 peptides. Score 0.628 Round 5: 334 peptides, 39 chains. Longest chain 25 peptides. Score 0.594 Taking the results from Round 4 Chains 43, Residues 318, Estimated correctness of the model 48.4 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 8276 restraints for refining 4154 atoms. 6854 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2974 (Rfree = 0.000) for 4154 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 22: After refmac, R = 0.2761 (Rfree = 0.000) for 4130 atoms. Found 28 (37 requested) and removed 23 (18 requested) atoms. Cycle 23: After refmac, R = 0.2678 (Rfree = 0.000) for 4109 atoms. Found 22 (37 requested) and removed 21 (18 requested) atoms. Cycle 24: After refmac, R = 0.2638 (Rfree = 0.000) for 4096 atoms. Found 19 (36 requested) and removed 19 (18 requested) atoms. Cycle 25: After refmac, R = 0.2601 (Rfree = 0.000) for 4091 atoms. Found 7 (36 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.71 2.60 Search for helices and strands: 0 residues in 0 chains, 4201 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 4207 seeds are put forward Round 1: 297 peptides, 39 chains. Longest chain 17 peptides. Score 0.523 Round 2: 329 peptides, 40 chains. Longest chain 18 peptides. Score 0.577 Round 3: 350 peptides, 41 chains. Longest chain 28 peptides. Score 0.606 Round 4: 338 peptides, 39 chains. Longest chain 26 peptides. Score 0.601 Round 5: 331 peptides, 35 chains. Longest chain 40 peptides. Score 0.621 Taking the results from Round 5 Chains 37, Residues 296, Estimated correctness of the model 46.6 % 4 chains (79 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 8100 restraints for refining 4183 atoms. 6657 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2950 (Rfree = 0.000) for 4183 atoms. Found 30 (37 requested) and removed 47 (18 requested) atoms. Cycle 27: After refmac, R = 0.2732 (Rfree = 0.000) for 4157 atoms. Found 13 (37 requested) and removed 23 (18 requested) atoms. Cycle 28: After refmac, R = 0.2662 (Rfree = 0.000) for 4145 atoms. Found 7 (37 requested) and removed 19 (18 requested) atoms. Cycle 29: After refmac, R = 0.2607 (Rfree = 0.000) for 4130 atoms. Found 6 (37 requested) and removed 18 (18 requested) atoms. Cycle 30: After refmac, R = 0.2568 (Rfree = 0.000) for 4114 atoms. Found 4 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.74 2.63 Search for helices and strands: 0 residues in 0 chains, 4205 seeds are put forward NCS extension: 46 residues added (18 deleted due to clashes), 4251 seeds are put forward Round 1: 275 peptides, 39 chains. Longest chain 19 peptides. Score 0.477 Round 2: 290 peptides, 37 chains. Longest chain 20 peptides. Score 0.528 Round 3: 288 peptides, 38 chains. Longest chain 19 peptides. Score 0.514 Round 4: 287 peptides, 36 chains. Longest chain 26 peptides. Score 0.531 Round 5: 280 peptides, 35 chains. Longest chain 23 peptides. Score 0.526 Taking the results from Round 4 Chains 37, Residues 251, Estimated correctness of the model 21.1 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 9119 restraints for refining 4180 atoms. 8025 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2987 (Rfree = 0.000) for 4180 atoms. Found 33 (37 requested) and removed 37 (18 requested) atoms. Cycle 32: After refmac, R = 0.2604 (Rfree = 0.000) for 4162 atoms. Found 20 (37 requested) and removed 27 (18 requested) atoms. Cycle 33: After refmac, R = 0.2509 (Rfree = 0.000) for 4148 atoms. Found 12 (37 requested) and removed 21 (18 requested) atoms. Cycle 34: After refmac, R = 0.2484 (Rfree = 0.000) for 4139 atoms. Found 7 (37 requested) and removed 19 (18 requested) atoms. Cycle 35: After refmac, R = 0.2474 (Rfree = 0.000) for 4122 atoms. Found 8 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.74 2.63 Search for helices and strands: 0 residues in 0 chains, 4245 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 4263 seeds are put forward Round 1: 259 peptides, 39 chains. Longest chain 27 peptides. Score 0.442 Round 2: 284 peptides, 37 chains. Longest chain 26 peptides. Score 0.515 Round 3: 281 peptides, 38 chains. Longest chain 17 peptides. Score 0.500 Round 4: 289 peptides, 36 chains. Longest chain 19 peptides. Score 0.535 Round 5: 287 peptides, 38 chains. Longest chain 22 peptides. Score 0.512 Taking the results from Round 4 Chains 37, Residues 253, Estimated correctness of the model 22.4 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 8949 restraints for refining 4151 atoms. 7868 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2858 (Rfree = 0.000) for 4151 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 37: After refmac, R = 0.2713 (Rfree = 0.000) for 4131 atoms. Found 24 (37 requested) and removed 24 (18 requested) atoms. Cycle 38: After refmac, R = 0.2666 (Rfree = 0.000) for 4124 atoms. Found 21 (37 requested) and removed 23 (18 requested) atoms. Cycle 39: After refmac, R = 0.2596 (Rfree = 0.000) for 4119 atoms. Found 11 (36 requested) and removed 18 (18 requested) atoms. Cycle 40: After refmac, R = 0.2590 (Rfree = 0.000) for 4108 atoms. Found 7 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.72 2.61 Search for helices and strands: 0 residues in 0 chains, 4239 seeds are put forward NCS extension: 0 residues added, 4239 seeds are put forward Round 1: 279 peptides, 42 chains. Longest chain 20 peptides. Score 0.457 Round 2: 297 peptides, 41 chains. Longest chain 18 peptides. Score 0.505 Round 3: 308 peptides, 41 chains. Longest chain 22 peptides. Score 0.527 Round 4: 308 peptides, 42 chains. Longest chain 27 peptides. Score 0.518 Round 5: 297 peptides, 43 chains. Longest chain 18 peptides. Score 0.486 Taking the results from Round 3 Chains 42, Residues 267, Estimated correctness of the model 19.9 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 8756 restraints for refining 4210 atoms. 7530 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2751 (Rfree = 0.000) for 4210 atoms. Found 37 (37 requested) and removed 26 (18 requested) atoms. Cycle 42: After refmac, R = 0.2776 (Rfree = 0.000) for 4208 atoms. Found 30 (37 requested) and removed 33 (18 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2555 (Rfree = 0.000) for 4195 atoms. Found 16 (37 requested) and removed 22 (18 requested) atoms. Cycle 44: After refmac, R = 0.2522 (Rfree = 0.000) for 4185 atoms. Found 14 (37 requested) and removed 20 (18 requested) atoms. Cycle 45: After refmac, R = 0.2480 (Rfree = 0.000) for 4179 atoms. Found 4 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.67 2.57 Search for helices and strands: 0 residues in 0 chains, 4307 seeds are put forward NCS extension: 0 residues added, 4307 seeds are put forward Round 1: 258 peptides, 39 chains. Longest chain 18 peptides. Score 0.439 Round 2: 279 peptides, 40 chains. Longest chain 18 peptides. Score 0.476 Round 3: 286 peptides, 35 chains. Longest chain 19 peptides. Score 0.538 Round 4: 275 peptides, 37 chains. Longest chain 16 peptides. Score 0.497 Round 5: 288 peptides, 37 chains. Longest chain 24 peptides. Score 0.524 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 251, Estimated correctness of the model 23.3 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (251 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12229 reflections ( 99.72 % complete ) and 9011 restraints for refining 4220 atoms. 7943 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2723 (Rfree = 0.000) for 4220 atoms. Found 0 (37 requested) and removed 16 (18 requested) atoms. Cycle 47: After refmac, R = 0.2736 (Rfree = 0.000) for 4191 atoms. Found 0 (37 requested) and removed 7 (18 requested) atoms. Cycle 48: After refmac, R = 0.2644 (Rfree = 0.000) for 4179 atoms. Found 0 (37 requested) and removed 12 (18 requested) atoms. Cycle 49: After refmac, R = 0.2668 (Rfree = 0.000) for 4161 atoms. Found 0 (37 requested) and removed 9 (18 requested) atoms. Writing output files ... TimeTaking 67.67