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 1vjv-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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/1vjv-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 19:28:06 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/1vjv-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 344 and 0 Target number of residues in the AU: 344 Target solvent content: 0.5708 Checking the provided sequence file Detected sequence length: 415 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 415 Adjusted target solvent content: 0.48 Input MTZ file: 1vjv-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: 19 Cell parameters: 49.299 81.862 107.491 90.000 90.000 90.000 Input sequence file: 1vjv-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3320 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 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 Loops will be built when appropriate and at the last cycle Resolution range: 65.126 3.200 Wilson plot Bfac: 41.90 7387 reflections ( 97.13 % complete ) and 0 restraints for refining 3689 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.2873 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2307 (Rfree = 0.000) for 3689 atoms. Found 33 (33 requested) and removed 47 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.81 2.89 Search for helices and strands: 0 residues in 0 chains, 3736 seeds are put forward Round 1: 227 peptides, 32 chains. Longest chain 15 peptides. Score 0.543 Round 2: 244 peptides, 28 chains. Longest chain 35 peptides. Score 0.640 Round 3: 264 peptides, 23 chains. Longest chain 49 peptides. Score 0.737 Round 4: 280 peptides, 23 chains. Longest chain 55 peptides. Score 0.767 Round 5: 277 peptides, 19 chains. Longest chain 51 peptides. Score 0.795 Taking the results from Round 5 Chains 20, Residues 258, Estimated correctness of the model 82.7 % 5 chains (146 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 232 A and 238 A 18 chains (260 residues) following loop building 4 chains (151 residues) in sequence following loop building ------------------------------------------------------ 7387 reflections ( 97.13 % complete ) and 4850 restraints for refining 3030 atoms. 3148 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2694 (Rfree = 0.000) for 3030 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 2: After refmac, R = 0.2431 (Rfree = 0.000) for 2966 atoms. Found 16 (26 requested) and removed 30 (13 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2275 (Rfree = 0.000) for 2933 atoms. Found 8 (25 requested) and removed 22 (13 requested) atoms. Cycle 4: After refmac, R = 0.2159 (Rfree = 0.000) for 2902 atoms. Found 10 (24 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2085 (Rfree = 0.000) for 2884 atoms. Found 6 (23 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.88 2.96 Search for helices and strands: 0 residues in 0 chains, 2964 seeds are put forward Round 1: 257 peptides, 22 chains. Longest chain 39 peptides. Score 0.733 Round 2: 265 peptides, 16 chains. Longest chain 51 peptides. Score 0.800 Round 3: 284 peptides, 16 chains. Longest chain 51 peptides. Score 0.827 Round 4: 278 peptides, 18 chains. Longest chain 54 peptides. Score 0.804 Round 5: 278 peptides, 19 chains. Longest chain 37 peptides. Score 0.796 Taking the results from Round 3 Chains 18, Residues 268, Estimated correctness of the model 87.3 % 6 chains (176 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 340 A and 343 A 17 chains (270 residues) following loop building 5 chains (178 residues) in sequence following loop building ------------------------------------------------------ 7387 reflections ( 97.13 % complete ) and 4509 restraints for refining 3030 atoms. 2630 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2576 (Rfree = 0.000) for 3030 atoms. Found 24 (24 requested) and removed 35 (13 requested) atoms. Cycle 7: After refmac, R = 0.2299 (Rfree = 0.000) for 2993 atoms. Found 13 (24 requested) and removed 26 (13 requested) atoms. Cycle 8: After refmac, R = 0.2239 (Rfree = 0.000) for 2967 atoms. Found 13 (22 requested) and removed 15 (13 requested) atoms. Cycle 9: After refmac, R = 0.2170 (Rfree = 0.000) for 2948 atoms. Found 15 (22 requested) and removed 14 (13 requested) atoms. Cycle 10: After refmac, R = 0.2078 (Rfree = 0.000) for 2937 atoms. Found 4 (21 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.89 2.97 Search for helices and strands: 0 residues in 0 chains, 2998 seeds are put forward Round 1: 259 peptides, 20 chains. Longest chain 39 peptides. Score 0.756 Round 2: 276 peptides, 20 chains. Longest chain 42 peptides. Score 0.785 Round 3: 277 peptides, 20 chains. Longest chain 41 peptides. Score 0.787 Round 4: 284 peptides, 22 chains. Longest chain 46 peptides. Score 0.782 Round 5: 285 peptides, 22 chains. Longest chain 50 peptides. Score 0.783 Taking the results from Round 3 Chains 21, Residues 257, Estimated correctness of the model 81.4 % 5 chains (118 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 235 A and 241 A 19 chains (261 residues) following loop building 4 chains (123 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7387 reflections ( 97.13 % complete ) and 5212 restraints for refining 3031 atoms. 3617 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2588 (Rfree = 0.000) for 3031 atoms. Found 21 (22 requested) and removed 32 (13 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2360 (Rfree = 0.000) for 2999 atoms. Found 11 (21 requested) and removed 16 (13 requested) atoms. Cycle 13: After refmac, R = 0.2269 (Rfree = 0.000) for 2981 atoms. Found 7 (20 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2220 (Rfree = 0.000) for 2953 atoms. Found 6 (19 requested) and removed 14 (13 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2439 (Rfree = 0.000) for 2937 atoms. Found 19 (19 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.85 2.93 Search for helices and strands: 0 residues in 0 chains, 3012 seeds are put forward Round 1: 258 peptides, 24 chains. Longest chain 25 peptides. Score 0.716 Round 2: 281 peptides, 22 chains. Longest chain 45 peptides. Score 0.777 Round 3: 281 peptides, 21 chains. Longest chain 34 peptides. Score 0.785 Round 4: 286 peptides, 23 chains. Longest chain 37 peptides. Score 0.777 Round 5: 281 peptides, 22 chains. Longest chain 32 peptides. Score 0.777 Taking the results from Round 3 Chains 22, Residues 260, Estimated correctness of the model 81.1 % 4 chains (82 residues) have been docked in sequence Building loops using Loopy2018 22 chains (260 residues) following loop building 4 chains (82 residues) in sequence following loop building ------------------------------------------------------ 7387 reflections ( 97.13 % complete ) and 5664 restraints for refining 3030 atoms. 4281 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2611 (Rfree = 0.000) for 3030 atoms. Found 19 (19 requested) and removed 30 (13 requested) atoms. Cycle 17: After refmac, R = 0.2379 (Rfree = 0.000) for 3007 atoms. Found 16 (18 requested) and removed 21 (13 requested) atoms. Cycle 18: After refmac, R = 0.2319 (Rfree = 0.000) for 2993 atoms. Found 10 (17 requested) and removed 15 (13 requested) atoms. Cycle 19: After refmac, R = 0.2250 (Rfree = 0.000) for 2982 atoms. Found 15 (17 requested) and removed 14 (13 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2177 (Rfree = 0.000) for 2978 atoms. Found 8 (16 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.86 2.94 Search for helices and strands: 0 residues in 0 chains, 3052 seeds are put forward Round 1: 252 peptides, 23 chains. Longest chain 25 peptides. Score 0.713 Round 2: 266 peptides, 25 chains. Longest chain 23 peptides. Score 0.722 Round 3: 282 peptides, 25 chains. Longest chain 26 peptides. Score 0.753 Round 4: 271 peptides, 24 chains. Longest chain 43 peptides. Score 0.741 Round 5: 281 peptides, 25 chains. Longest chain 39 peptides. Score 0.751 Taking the results from Round 3 Chains 27, Residues 257, Estimated correctness of the model 75.6 % 5 chains (104 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 235 A and 241 A 25 chains (260 residues) following loop building 4 chains (109 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7387 reflections ( 97.13 % complete ) and 5228 restraints for refining 3031 atoms. 3734 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2662 (Rfree = 0.000) for 3031 atoms. Found 16 (16 requested) and removed 28 (13 requested) atoms. Cycle 22: After refmac, R = 0.2311 (Rfree = 0.000) for 3008 atoms. Found 16 (16 requested) and removed 22 (13 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2241 (Rfree = 0.000) for 2995 atoms. Found 11 (15 requested) and removed 17 (13 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2190 (Rfree = 0.000) for 2985 atoms. Found 9 (14 requested) and removed 15 (13 requested) atoms. Cycle 25: After refmac, R = 0.2304 (Rfree = 0.000) for 2974 atoms. Found 14 (14 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.81 2.89 Search for helices and strands: 0 residues in 0 chains, 3041 seeds are put forward Round 1: 241 peptides, 26 chains. Longest chain 23 peptides. Score 0.656 Round 2: 262 peptides, 23 chains. Longest chain 28 peptides. Score 0.733 Round 3: 257 peptides, 21 chains. Longest chain 38 peptides. Score 0.743 Round 4: 256 peptides, 28 chains. Longest chain 26 peptides. Score 0.669 Round 5: 261 peptides, 25 chains. Longest chain 22 peptides. Score 0.712 Taking the results from Round 3 Chains 23, Residues 236, Estimated correctness of the model 73.8 % 5 chains (123 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 235 A and 240 A 22 chains (240 residues) following loop building 4 chains (127 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7387 reflections ( 97.13 % complete ) and 5213 restraints for refining 3031 atoms. 3703 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2466 (Rfree = 0.000) for 3031 atoms. Found 13 (13 requested) and removed 33 (13 requested) atoms. Cycle 27: After refmac, R = 0.2363 (Rfree = 0.000) for 2993 atoms. Found 13 (13 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2305 (Rfree = 0.000) for 2977 atoms. Found 13 (13 requested) and removed 14 (13 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2113 (Rfree = 0.000) for 2968 atoms. Found 11 (13 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.2067 (Rfree = 0.000) for 2959 atoms. Found 10 (13 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.89 2.97 Search for helices and strands: 0 residues in 0 chains, 3027 seeds are put forward Round 1: 249 peptides, 30 chains. Longest chain 23 peptides. Score 0.630 Round 2: 257 peptides, 25 chains. Longest chain 31 peptides. Score 0.703 Round 3: 267 peptides, 26 chains. Longest chain 30 peptides. Score 0.714 Round 4: 266 peptides, 27 chains. Longest chain 25 peptides. Score 0.702 Round 5: 279 peptides, 25 chains. Longest chain 28 peptides. Score 0.747 Taking the results from Round 5 Chains 29, Residues 254, Estimated correctness of the model 74.5 % 6 chains (112 residues) have been docked in sequence Building loops using Loopy2018 29 chains (254 residues) following loop building 6 chains (112 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7387 reflections ( 97.13 % complete ) and 5166 restraints for refining 3031 atoms. 3656 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2689 (Rfree = 0.000) for 3031 atoms. Found 13 (13 requested) and removed 23 (13 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2519 (Rfree = 0.000) for 3011 atoms. Found 13 (13 requested) and removed 13 (13 requested) atoms. Cycle 33: After refmac, R = 0.2438 (Rfree = 0.000) for 3005 atoms. Found 13 (13 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.2379 (Rfree = 0.000) for 3004 atoms. Found 9 (13 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2299 (Rfree = 0.000) for 2996 atoms. Found 1 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.88 2.96 Search for helices and strands: 0 residues in 0 chains, 3048 seeds are put forward Round 1: 244 peptides, 33 chains. Longest chain 23 peptides. Score 0.580 Round 2: 267 peptides, 26 chains. Longest chain 24 peptides. Score 0.714 Round 3: 260 peptides, 28 chains. Longest chain 36 peptides. Score 0.679 Round 4: 254 peptides, 29 chains. Longest chain 24 peptides. Score 0.654 Round 5: 257 peptides, 28 chains. Longest chain 32 peptides. Score 0.672 Taking the results from Round 2 Chains 30, Residues 241, Estimated correctness of the model 68.1 % 5 chains (84 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 235 A and 241 A Built loop between residues 262 A and 265 A 28 chains (247 residues) following loop building 3 chains (91 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7387 reflections ( 97.13 % complete ) and 5503 restraints for refining 3031 atoms. 4134 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2570 (Rfree = 0.000) for 3031 atoms. Found 13 (13 requested) and removed 21 (13 requested) atoms. Cycle 37: After refmac, R = 0.2422 (Rfree = 0.000) for 3012 atoms. Found 13 (13 requested) and removed 14 (13 requested) atoms. Cycle 38: After refmac, R = 0.2312 (Rfree = 0.000) for 3010 atoms. Found 13 (13 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.2277 (Rfree = 0.000) for 3006 atoms. Found 7 (13 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2141 (Rfree = 0.000) for 2996 atoms. Found 9 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.89 2.97 Search for helices and strands: 0 residues in 0 chains, 3059 seeds are put forward Round 1: 246 peptides, 32 chains. Longest chain 23 peptides. Score 0.598 Round 2: 261 peptides, 29 chains. Longest chain 43 peptides. Score 0.670 Round 3: 260 peptides, 29 chains. Longest chain 26 peptides. Score 0.668 Round 4: 257 peptides, 28 chains. Longest chain 26 peptides. Score 0.672 Round 5: 262 peptides, 30 chains. Longest chain 25 peptides. Score 0.662 Taking the results from Round 4 Chains 29, Residues 229, Estimated correctness of the model 59.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7387 reflections ( 97.13 % complete ) and 6441 restraints for refining 3031 atoms. 5433 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2427 (Rfree = 0.000) for 3031 atoms. Found 13 (13 requested) and removed 24 (13 requested) atoms. Cycle 42: After refmac, R = 0.2266 (Rfree = 0.000) for 3010 atoms. Found 13 (13 requested) and removed 18 (13 requested) atoms. Cycle 43: After refmac, R = 0.2137 (Rfree = 0.000) for 3001 atoms. Found 12 (13 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.2128 (Rfree = 0.000) for 2997 atoms. Found 5 (13 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.2107 (Rfree = 0.000) for 2987 atoms. Found 7 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.92 3.00 Search for helices and strands: 0 residues in 0 chains, 3030 seeds are put forward Round 1: 210 peptides, 28 chains. Longest chain 22 peptides. Score 0.545 Round 2: 232 peptides, 26 chains. Longest chain 23 peptides. Score 0.633 Round 3: 230 peptides, 25 chains. Longest chain 38 peptides. Score 0.640 Round 4: 230 peptides, 24 chains. Longest chain 25 peptides. Score 0.652 Round 5: 227 peptides, 27 chains. Longest chain 22 peptides. Score 0.608 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 206, Estimated correctness of the model 54.3 % 5 chains (58 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 1vjv-3_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (206 residues) following loop building 5 chains (58 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7387 reflections ( 97.13 % complete ) and 6085 restraints for refining 3031 atoms. 5033 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2333 (Rfree = 0.000) for 3031 atoms. Found 0 (13 requested) and removed 9 (13 requested) atoms. Cycle 47: After refmac, R = 0.2272 (Rfree = 0.000) for 3006 atoms. Found 0 (13 requested) and removed 7 (13 requested) atoms. Cycle 48: After refmac, R = 0.2219 (Rfree = 0.000) for 2996 atoms. Found 0 (13 requested) and removed 2 (13 requested) atoms. Cycle 49: After refmac, R = 0.2158 (Rfree = 0.000) for 2990 atoms. Found 0 (13 requested) and removed 2 (13 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 58.14