Sun 23 Dec 22:23:10 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 1vjr-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjr-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-4.0-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/1vjr-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-4.0-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 ============================================================ Sun 23 Dec 22:23:20 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/1vjr-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjr-4.0-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 438 and 0 Target number of residues in the AU: 438 Target solvent content: 0.6654 Checking the provided sequence file Detected sequence length: 271 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 542 Adjusted target solvent content: 0.59 Input MTZ file: 1vjr-4.0-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: 92 Cell parameters: 93.998 93.998 160.365 90.000 90.000 90.000 Input sequence file: 1vjr-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4336 target number of atoms Had to go as low as 0.65 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: 81.094 4.000 Wilson plot Bfac: 88.87 6517 reflections ( 99.89 % complete ) and 0 restraints for refining 4810 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3515 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3356 (Rfree = 0.000) for 4810 atoms. Found 22 (22 requested) and removed 124 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.32 Search for helices and strands: 0 residues in 0 chains, 4745 seeds are put forward NCS extension: 0 residues added, 4745 seeds are put forward Round 1: 156 peptides, 26 chains. Longest chain 11 peptides. Score 0.327 Round 2: 189 peptides, 22 chains. Longest chain 14 peptides. Score 0.454 Round 3: 186 peptides, 19 chains. Longest chain 26 peptides. Score 0.480 Round 4: 188 peptides, 18 chains. Longest chain 25 peptides. Score 0.495 Round 5: 194 peptides, 18 chains. Longest chain 26 peptides. Score 0.508 Taking the results from Round 5 Chains 19, Residues 176, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 7661 restraints for refining 3431 atoms. 6858 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3040 (Rfree = 0.000) for 3431 atoms. Found 16 (16 requested) and removed 88 (8 requested) atoms. Cycle 2: After refmac, R = 0.2781 (Rfree = 0.000) for 3274 atoms. Found 15 (15 requested) and removed 51 (7 requested) atoms. Cycle 3: After refmac, R = 0.2764 (Rfree = 0.000) for 3160 atoms. Found 15 (15 requested) and removed 45 (7 requested) atoms. Cycle 4: After refmac, R = 0.2634 (Rfree = 0.000) for 3075 atoms. Found 14 (14 requested) and removed 41 (7 requested) atoms. Cycle 5: After refmac, R = 0.2533 (Rfree = 0.000) for 3000 atoms. Found 14 (14 requested) and removed 39 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.30 Search for helices and strands: 0 residues in 0 chains, 3049 seeds are put forward NCS extension: 0 residues added, 3049 seeds are put forward Round 1: 185 peptides, 21 chains. Longest chain 22 peptides. Score 0.456 Round 2: 201 peptides, 20 chains. Longest chain 23 peptides. Score 0.501 Round 3: 199 peptides, 21 chains. Longest chain 28 peptides. Score 0.487 Round 4: 180 peptides, 17 chains. Longest chain 23 peptides. Score 0.489 Round 5: 190 peptides, 19 chains. Longest chain 27 peptides. Score 0.489 Taking the results from Round 2 Chains 21, Residues 181, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 5989 restraints for refining 2920 atoms. 5243 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2778 (Rfree = 0.000) for 2920 atoms. Found 13 (13 requested) and removed 39 (6 requested) atoms. Cycle 7: After refmac, R = 0.2621 (Rfree = 0.000) for 2843 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 8: After refmac, R = 0.2503 (Rfree = 0.000) for 2806 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 9: After refmac, R = 0.2501 (Rfree = 0.000) for 2769 atoms. Found 13 (13 requested) and removed 41 (6 requested) atoms. Cycle 10: After refmac, R = 0.2367 (Rfree = 0.000) for 2728 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.34 Search for helices and strands: 0 residues in 0 chains, 2805 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 2835 seeds are put forward Round 1: 186 peptides, 25 chains. Longest chain 18 peptides. Score 0.414 Round 2: 197 peptides, 20 chains. Longest chain 27 peptides. Score 0.493 Round 3: 181 peptides, 21 chains. Longest chain 20 peptides. Score 0.447 Round 4: 202 peptides, 17 chains. Longest chain 29 peptides. Score 0.534 Round 5: 184 peptides, 19 chains. Longest chain 22 peptides. Score 0.475 Taking the results from Round 4 Chains 20, Residues 185, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 5753 restraints for refining 2896 atoms. 4961 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2776 (Rfree = 0.000) for 2896 atoms. Found 13 (13 requested) and removed 42 (6 requested) atoms. Cycle 12: After refmac, R = 0.2469 (Rfree = 0.000) for 2830 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 13: After refmac, R = 0.2467 (Rfree = 0.000) for 2798 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.2524 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 15: After refmac, R = 0.2350 (Rfree = 0.000) for 2763 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.40 Search for helices and strands: 0 residues in 0 chains, 2851 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2868 seeds are put forward Round 1: 184 peptides, 21 chains. Longest chain 16 peptides. Score 0.454 Round 2: 218 peptides, 21 chains. Longest chain 39 peptides. Score 0.526 Round 3: 198 peptides, 18 chains. Longest chain 38 peptides. Score 0.516 Round 4: 211 peptides, 19 chains. Longest chain 32 peptides. Score 0.532 Round 5: 194 peptides, 19 chains. Longest chain 33 peptides. Score 0.497 Taking the results from Round 4 Chains 22, Residues 192, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 6008 restraints for refining 2936 atoms. 5206 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2525 (Rfree = 0.000) for 2936 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 17: After refmac, R = 0.2312 (Rfree = 0.000) for 2903 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 18: After refmac, R = 0.2434 (Rfree = 0.000) for 2884 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 19: After refmac, R = 0.2303 (Rfree = 0.000) for 2863 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 20: After refmac, R = 0.2326 (Rfree = 0.000) for 2849 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.34 Search for helices and strands: 0 residues in 0 chains, 2966 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 2999 seeds are put forward Round 1: 193 peptides, 21 chains. Longest chain 33 peptides. Score 0.474 Round 2: 195 peptides, 20 chains. Longest chain 30 peptides. Score 0.489 Round 3: 185 peptides, 18 chains. Longest chain 26 peptides. Score 0.489 Round 4: 194 peptides, 18 chains. Longest chain 23 peptides. Score 0.508 Round 5: 196 peptides, 19 chains. Longest chain 28 peptides. Score 0.501 Taking the results from Round 4 Chains 19, Residues 176, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 6397 restraints for refining 3002 atoms. 5688 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2624 (Rfree = 0.000) for 3002 atoms. Found 14 (14 requested) and removed 34 (7 requested) atoms. Cycle 22: After refmac, R = 0.2458 (Rfree = 0.000) for 2948 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 23: After refmac, R = 0.2373 (Rfree = 0.000) for 2892 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 24: After refmac, R = 0.2461 (Rfree = 0.000) for 2872 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 25: After refmac, R = 0.2326 (Rfree = 0.000) for 2835 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.23 Search for helices and strands: 0 residues in 0 chains, 2885 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2909 seeds are put forward Round 1: 193 peptides, 29 chains. Longest chain 22 peptides. Score 0.386 Round 2: 203 peptides, 23 chains. Longest chain 26 peptides. Score 0.474 Round 3: 210 peptides, 28 chains. Longest chain 18 peptides. Score 0.437 Round 4: 210 peptides, 26 chains. Longest chain 23 peptides. Score 0.458 Round 5: 210 peptides, 23 chains. Longest chain 24 peptides. Score 0.489 Taking the results from Round 5 Chains 24, Residues 187, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 6663 restraints for refining 3126 atoms. 5836 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2385 (Rfree = 0.000) for 3126 atoms. Found 14 (14 requested) and removed 42 (7 requested) atoms. Cycle 27: After refmac, R = 0.2294 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. Cycle 28: After refmac, R = 0.2331 (Rfree = 0.000) for 3015 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2184 (Rfree = 0.000) for 2995 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 30: After refmac, R = 0.2184 (Rfree = 0.000) for 2972 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.34 Search for helices and strands: 0 residues in 0 chains, 3082 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 3110 seeds are put forward Round 1: 188 peptides, 29 chains. Longest chain 16 peptides. Score 0.374 Round 2: 205 peptides, 23 chains. Longest chain 27 peptides. Score 0.479 Round 3: 198 peptides, 24 chains. Longest chain 19 peptides. Score 0.453 Round 4: 218 peptides, 23 chains. Longest chain 22 peptides. Score 0.506 Round 5: 224 peptides, 25 chains. Longest chain 23 peptides. Score 0.499 Taking the results from Round 4 Chains 25, Residues 195, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 6925 restraints for refining 3151 atoms. 6143 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2535 (Rfree = 0.000) for 3151 atoms. Found 14 (14 requested) and removed 48 (7 requested) atoms. Cycle 32: After refmac, R = 0.2396 (Rfree = 0.000) for 3082 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 33: After refmac, R = 0.2334 (Rfree = 0.000) for 3051 atoms. Found 14 (14 requested) and removed 35 (7 requested) atoms. Cycle 34: After refmac, R = 0.2261 (Rfree = 0.000) for 3019 atoms. Found 13 (14 requested) and removed 27 (7 requested) atoms. Cycle 35: After refmac, R = 0.2237 (Rfree = 0.000) for 2996 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.38 Search for helices and strands: 0 residues in 0 chains, 3082 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3115 seeds are put forward Round 1: 175 peptides, 28 chains. Longest chain 13 peptides. Score 0.353 Round 2: 203 peptides, 24 chains. Longest chain 20 peptides. Score 0.464 Round 3: 207 peptides, 25 chains. Longest chain 18 peptides. Score 0.462 Round 4: 207 peptides, 24 chains. Longest chain 19 peptides. Score 0.472 Round 5: 196 peptides, 22 chains. Longest chain 17 peptides. Score 0.470 Taking the results from Round 4 Chains 26, Residues 183, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 6478 restraints for refining 3114 atoms. 5650 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2472 (Rfree = 0.000) for 3114 atoms. Found 14 (14 requested) and removed 50 (7 requested) atoms. Cycle 37: After refmac, R = 0.2267 (Rfree = 0.000) for 3044 atoms. Found 14 (14 requested) and removed 39 (7 requested) atoms. Cycle 38: After refmac, R = 0.2337 (Rfree = 0.000) for 2997 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 39: After refmac, R = 0.2301 (Rfree = 0.000) for 2964 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 40: After refmac, R = 0.2247 (Rfree = 0.000) for 2949 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.38 Search for helices and strands: 0 residues in 0 chains, 3051 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3073 seeds are put forward Round 1: 181 peptides, 28 chains. Longest chain 15 peptides. Score 0.368 Round 2: 204 peptides, 26 chains. Longest chain 26 peptides. Score 0.445 Round 3: 205 peptides, 26 chains. Longest chain 20 peptides. Score 0.447 Round 4: 221 peptides, 25 chains. Longest chain 29 peptides. Score 0.492 Round 5: 216 peptides, 23 chains. Longest chain 21 peptides. Score 0.502 Taking the results from Round 5 Chains 26, Residues 193, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6517 reflections ( 99.89 % complete ) and 6530 restraints for refining 3114 atoms. 5719 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2565 (Rfree = 0.000) for 3114 atoms. Found 14 (14 requested) and removed 55 (7 requested) atoms. Cycle 42: After refmac, R = 0.2435 (Rfree = 0.000) for 3035 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 43: After refmac, R = 0.2476 (Rfree = 0.000) for 3003 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 44: After refmac, R = 0.2356 (Rfree = 0.000) for 2965 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 45: After refmac, R = 0.2335 (Rfree = 0.000) for 2940 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.31 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3072 seeds are put forward Round 1: 182 peptides, 28 chains. Longest chain 21 peptides. Score 0.370 Round 2: 191 peptides, 22 chains. Longest chain 25 peptides. Score 0.458 Round 3: 173 peptides, 21 chains. Longest chain 22 peptides. Score 0.428 Round 4: 205 peptides, 23 chains. Longest chain 28 peptides. Score 0.479 Round 5: 206 peptides, 22 chains. Longest chain 25 peptides. Score 0.491 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 184, 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 1vjr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6517 reflections ( 99.89 % complete ) and 6822 restraints for refining 3016 atoms. 6108 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2306 (Rfree = 0.000) for 3016 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2307 (Rfree = 0.000) for 2974 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2327 (Rfree = 0.000) for 2948 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2455 (Rfree = 0.000) for 2916 atoms. TimeTaking 58.27