Tue 25 Dec 19:27:55 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 1vp7-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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/1vp7-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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 19:28:05 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/1vp7-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.2-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 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-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: 1vp7-3.2-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 3.200 Wilson plot Bfac: 30.03 12229 reflections ( 99.72 % complete ) and 0 restraints for refining 5314 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3134 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2803 (Rfree = 0.000) for 5314 atoms. Found 47 (47 requested) and removed 44 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.73 2.62 Search for helices and strands: 0 residues in 0 chains, 5435 seeds are put forward NCS extension: 0 residues added, 5435 seeds are put forward Round 1: 275 peptides, 37 chains. Longest chain 19 peptides. Score 0.497 Round 2: 310 peptides, 37 chains. Longest chain 23 peptides. Score 0.567 Round 3: 320 peptides, 35 chains. Longest chain 29 peptides. Score 0.602 Round 4: 330 peptides, 38 chains. Longest chain 27 peptides. Score 0.595 Round 5: 328 peptides, 36 chains. Longest chain 26 peptides. Score 0.608 Taking the results from Round 5 Chains 36, Residues 292, Estimated correctness of the model 43.2 % 6 chains (97 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7996 restraints for refining 4218 atoms. 6477 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2791 (Rfree = 0.000) for 4218 atoms. Found 37 (37 requested) and removed 49 (18 requested) atoms. Cycle 2: After refmac, R = 0.2597 (Rfree = 0.000) for 4139 atoms. Found 34 (37 requested) and removed 33 (18 requested) atoms. Cycle 3: After refmac, R = 0.2515 (Rfree = 0.000) for 4115 atoms. Found 20 (37 requested) and removed 30 (18 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2473 (Rfree = 0.000) for 4094 atoms. Found 13 (36 requested) and removed 22 (18 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2435 (Rfree = 0.000) for 4073 atoms. Found 11 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.69 2.58 Search for helices and strands: 0 residues in 0 chains, 4211 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 4221 seeds are put forward Round 1: 303 peptides, 34 chains. Longest chain 20 peptides. Score 0.580 Round 2: 335 peptides, 28 chains. Longest chain 33 peptides. Score 0.681 Round 3: 330 peptides, 29 chains. Longest chain 36 peptides. Score 0.666 Round 4: 328 peptides, 34 chains. Longest chain 26 peptides. Score 0.624 Round 5: 343 peptides, 31 chains. Longest chain 30 peptides. Score 0.671 Taking the results from Round 2 Chains 30, Residues 307, Estimated correctness of the model 61.0 % 6 chains (130 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7283 restraints for refining 4095 atoms. 5587 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2786 (Rfree = 0.000) for 4095 atoms. Found 36 (36 requested) and removed 48 (18 requested) atoms. Cycle 7: After refmac, R = 0.2666 (Rfree = 0.000) for 4055 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2580 (Rfree = 0.000) for 4050 atoms. Found 10 (36 requested) and removed 20 (18 requested) atoms. Cycle 9: After refmac, R = 0.2553 (Rfree = 0.000) for 4025 atoms. Found 19 (36 requested) and removed 18 (18 requested) atoms. Cycle 10: After refmac, R = 0.2513 (Rfree = 0.000) for 4020 atoms. Found 9 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.65 2.55 Search for helices and strands: 0 residues in 0 chains, 4158 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 4168 seeds are put forward Round 1: 311 peptides, 36 chains. Longest chain 27 peptides. Score 0.577 Round 2: 327 peptides, 33 chains. Longest chain 22 peptides. Score 0.630 Round 3: 330 peptides, 37 chains. Longest chain 33 peptides. Score 0.603 Round 4: 328 peptides, 34 chains. Longest chain 33 peptides. Score 0.624 Round 5: 328 peptides, 35 chains. Longest chain 24 peptides. Score 0.616 Taking the results from Round 2 Chains 35, Residues 294, Estimated correctness of the model 48.9 % 8 chains (137 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12229 reflections ( 99.72 % complete ) and 7225 restraints for refining 4055 atoms. 5549 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2900 (Rfree = 0.000) for 4055 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2775 (Rfree = 0.000) for 4034 atoms. Found 33 (36 requested) and removed 27 (18 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2719 (Rfree = 0.000) for 4034 atoms. Found 11 (36 requested) and removed 20 (18 requested) atoms. Cycle 14: After refmac, R = 0.2663 (Rfree = 0.000) for 4022 atoms. Found 6 (36 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2638 (Rfree = 0.000) for 4003 atoms. Found 14 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.65 2.55 Search for helices and strands: 0 residues in 0 chains, 4124 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 4133 seeds are put forward Round 1: 308 peptides, 35 chains. Longest chain 22 peptides. Score 0.580 Round 2: 319 peptides, 33 chains. Longest chain 22 peptides. Score 0.617 Round 3: 320 peptides, 32 chains. Longest chain 25 peptides. Score 0.626 Round 4: 309 peptides, 31 chains. Longest chain 26 peptides. Score 0.616 Round 5: 314 peptides, 35 chains. Longest chain 25 peptides. Score 0.591 Taking the results from Round 3 Chains 35, Residues 288, Estimated correctness of the model 47.9 % 7 chains (105 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12229 reflections ( 99.72 % complete ) and 7565 restraints for refining 4040 atoms. 6041 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2912 (Rfree = 0.000) for 4040 atoms. Found 36 (36 requested) and removed 42 (18 requested) atoms. Cycle 17: After refmac, R = 0.2797 (Rfree = 0.000) for 4024 atoms. Found 21 (36 requested) and removed 24 (18 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2740 (Rfree = 0.000) for 4019 atoms. Found 8 (36 requested) and removed 23 (18 requested) atoms. Cycle 19: After refmac, R = 0.2702 (Rfree = 0.000) for 4001 atoms. Found 7 (35 requested) and removed 21 (17 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2653 (Rfree = 0.000) for 3980 atoms. Found 9 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.64 2.54 Search for helices and strands: 0 residues in 0 chains, 4105 seeds are put forward NCS extension: 5 residues added (3 deleted due to clashes), 4110 seeds are put forward Round 1: 296 peptides, 32 chains. Longest chain 27 peptides. Score 0.584 Round 2: 308 peptides, 28 chains. Longest chain 34 peptides. Score 0.638 Round 3: 321 peptides, 28 chains. Longest chain 38 peptides. Score 0.659 Round 4: 318 peptides, 31 chains. Longest chain 34 peptides. Score 0.631 Round 5: 313 peptides, 32 chains. Longest chain 23 peptides. Score 0.614 Taking the results from Round 3 Chains 31, Residues 293, Estimated correctness of the model 56.0 % 7 chains (126 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7219 restraints for refining 4051 atoms. 5578 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2908 (Rfree = 0.000) for 4051 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 22: After refmac, R = 0.2753 (Rfree = 0.000) for 4038 atoms. Found 20 (36 requested) and removed 24 (18 requested) atoms. Cycle 23: After refmac, R = 0.2700 (Rfree = 0.000) for 4026 atoms. Found 9 (36 requested) and removed 20 (18 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2739 (Rfree = 0.000) for 4012 atoms. Found 7 (36 requested) and removed 21 (18 requested) atoms. Cycle 25: After refmac, R = 0.2747 (Rfree = 0.000) for 3998 atoms. Found 8 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.62 2.52 Search for helices and strands: 0 residues in 0 chains, 4093 seeds are put forward NCS extension: 0 residues added (3 deleted due to clashes), 4093 seeds are put forward Round 1: 293 peptides, 32 chains. Longest chain 31 peptides. Score 0.578 Round 2: 302 peptides, 33 chains. Longest chain 32 peptides. Score 0.586 Round 3: 304 peptides, 32 chains. Longest chain 32 peptides. Score 0.599 Round 4: 301 peptides, 34 chains. Longest chain 19 peptides. Score 0.576 Round 5: 289 peptides, 33 chains. Longest chain 32 peptides. Score 0.562 Taking the results from Round 3 Chains 37, Residues 272, Estimated correctness of the model 40.8 % 7 chains (115 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7514 restraints for refining 4074 atoms. 6021 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2921 (Rfree = 0.000) for 4074 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 27: After refmac, R = 0.2784 (Rfree = 0.000) for 4044 atoms. Found 19 (36 requested) and removed 20 (18 requested) atoms. Cycle 28: After refmac, R = 0.2707 (Rfree = 0.000) for 4026 atoms. Found 17 (36 requested) and removed 19 (18 requested) atoms. Cycle 29: After refmac, R = 0.2688 (Rfree = 0.000) for 4017 atoms. Found 17 (36 requested) and removed 19 (18 requested) atoms. Cycle 30: After refmac, R = 0.2671 (Rfree = 0.000) for 4013 atoms. Found 11 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.64 2.54 Search for helices and strands: 0 residues in 0 chains, 4148 seeds are put forward NCS extension: 6 residues added (6 deleted due to clashes), 4154 seeds are put forward Round 1: 287 peptides, 36 chains. Longest chain 18 peptides. Score 0.531 Round 2: 295 peptides, 38 chains. Longest chain 28 peptides. Score 0.529 Round 3: 295 peptides, 34 chains. Longest chain 29 peptides. Score 0.565 Round 4: 303 peptides, 34 chains. Longest chain 31 peptides. Score 0.580 Round 5: 305 peptides, 34 chains. Longest chain 27 peptides. Score 0.583 Taking the results from Round 5 Chains 34, Residues 271, Estimated correctness of the model 36.4 % 4 chains (83 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7809 restraints for refining 4097 atoms. 6436 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2887 (Rfree = 0.000) for 4097 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 32: After refmac, R = 0.2656 (Rfree = 0.000) for 4080 atoms. Found 21 (36 requested) and removed 26 (18 requested) atoms. Cycle 33: After refmac, R = 0.2541 (Rfree = 0.000) for 4065 atoms. Found 17 (36 requested) and removed 23 (18 requested) atoms. Cycle 34: After refmac, R = 0.2476 (Rfree = 0.000) for 4052 atoms. Found 11 (36 requested) and removed 19 (18 requested) atoms. Cycle 35: After refmac, R = 0.2419 (Rfree = 0.000) for 4040 atoms. Found 13 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.64 2.54 Search for helices and strands: 0 residues in 0 chains, 4178 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 4189 seeds are put forward Round 1: 280 peptides, 35 chains. Longest chain 27 peptides. Score 0.526 Round 2: 310 peptides, 29 chains. Longest chain 35 peptides. Score 0.634 Round 3: 321 peptides, 32 chains. Longest chain 36 peptides. Score 0.628 Round 4: 305 peptides, 34 chains. Longest chain 33 peptides. Score 0.583 Round 5: 321 peptides, 32 chains. Longest chain 36 peptides. Score 0.628 Taking the results from Round 2 Chains 29, Residues 281, Estimated correctness of the model 49.9 % 7 chains (140 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7206 restraints for refining 4134 atoms. 5562 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2695 (Rfree = 0.000) for 4134 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 37: After refmac, R = 0.2562 (Rfree = 0.000) for 4115 atoms. Found 19 (37 requested) and removed 23 (18 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2506 (Rfree = 0.000) for 4096 atoms. Found 15 (36 requested) and removed 18 (18 requested) atoms. Cycle 39: After refmac, R = 0.2432 (Rfree = 0.000) for 4086 atoms. Found 11 (36 requested) and removed 20 (18 requested) atoms. Cycle 40: After refmac, R = 0.2360 (Rfree = 0.000) for 4071 atoms. Found 10 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.62 2.52 Search for helices and strands: 0 residues in 0 chains, 4179 seeds are put forward NCS extension: 0 residues added, 4179 seeds are put forward Round 1: 296 peptides, 34 chains. Longest chain 34 peptides. Score 0.567 Round 2: 303 peptides, 34 chains. Longest chain 36 peptides. Score 0.580 Round 3: 295 peptides, 34 chains. Longest chain 46 peptides. Score 0.565 Round 4: 307 peptides, 33 chains. Longest chain 24 peptides. Score 0.596 Round 5: 302 peptides, 32 chains. Longest chain 31 peptides. Score 0.595 Taking the results from Round 4 Chains 34, Residues 274, Estimated correctness of the model 40.0 % 5 chains (96 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.72 % complete ) and 7765 restraints for refining 4109 atoms. 6328 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2793 (Rfree = 0.000) for 4109 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. Cycle 42: After refmac, R = 0.2615 (Rfree = 0.000) for 4096 atoms. Found 20 (36 requested) and removed 23 (18 requested) atoms. Cycle 43: After refmac, R = 0.2547 (Rfree = 0.000) for 4080 atoms. Found 9 (36 requested) and removed 21 (18 requested) atoms. Cycle 44: After refmac, R = 0.2526 (Rfree = 0.000) for 4058 atoms. Found 16 (36 requested) and removed 19 (18 requested) atoms. Cycle 45: After refmac, R = 0.2519 (Rfree = 0.000) for 4045 atoms. Found 16 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.62 2.52 Search for helices and strands: 0 residues in 0 chains, 4200 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 4214 seeds are put forward Round 1: 281 peptides, 33 chains. Longest chain 27 peptides. Score 0.546 Round 2: 294 peptides, 31 chains. Longest chain 26 peptides. Score 0.589 Round 3: 300 peptides, 31 chains. Longest chain 25 peptides. Score 0.600 Round 4: 288 peptides, 32 chains. Longest chain 33 peptides. Score 0.569 Round 5: 295 peptides, 28 chains. Longest chain 32 peptides. Score 0.616 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 267, Estimated correctness of the model 45.3 % 4 chains (94 residues) have been docked in sequence Sequence coverage is 35 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (267 residues) following loop building 4 chains (94 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12229 reflections ( 99.72 % complete ) and 7653 restraints for refining 4100 atoms. 6239 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2708 (Rfree = 0.000) for 4100 atoms. Found 0 (36 requested) and removed 5 (18 requested) atoms. Cycle 47: After refmac, R = 0.2605 (Rfree = 0.000) for 4083 atoms. Found 0 (36 requested) and removed 3 (18 requested) atoms. Cycle 48: After refmac, R = 0.2633 (Rfree = 0.000) for 4077 atoms. Found 0 (36 requested) and removed 2 (18 requested) atoms. Cycle 49: After refmac, R = 0.2580 (Rfree = 0.000) for 4072 atoms. Found 0 (36 requested) and removed 0 (18 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:04:48 GMT 2018 Job finished. TimeTaking 96.87