null Sun 23 Dec 22:23:02 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 2obp-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obp-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obp-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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/2obp-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 22:23:12 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/2obp-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6861 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.56 Input MTZ file: 2obp-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.75 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: 29.462 4.001 Wilson plot Bfac: 105.46 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2299 reflections ( 99.14 % complete ) and 0 restraints for refining 1700 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3781 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4027 (Rfree = 0.000) for 1700 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.25 3.92 Search for helices and strands: 0 residues in 0 chains, 1731 seeds are put forward NCS extension: 0 residues added, 1731 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 9 peptides. Score 0.265 Round 2: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.324 Round 3: 75 peptides, 11 chains. Longest chain 10 peptides. Score 0.420 Round 4: 75 peptides, 11 chains. Longest chain 12 peptides. Score 0.420 Round 5: 79 peptides, 9 chains. Longest chain 17 peptides. Score 0.508 Taking the results from Round 5 Chains 9, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 3146 restraints for refining 1319 atoms. 2875 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3521 (Rfree = 0.000) for 1319 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 2: After refmac, R = 0.3471 (Rfree = 0.000) for 1274 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 3: After refmac, R = 0.3376 (Rfree = 0.000) for 1229 atoms. Found 4 (5 requested) and removed 17 (2 requested) atoms. Cycle 4: After refmac, R = 0.3145 (Rfree = 0.000) for 1190 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 5: After refmac, R = 0.3070 (Rfree = 0.000) for 1164 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.08 3.77 Search for helices and strands: 0 residues in 0 chains, 1196 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1221 seeds are put forward Round 1: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.347 Round 2: 76 peptides, 12 chains. Longest chain 14 peptides. Score 0.396 Round 3: 88 peptides, 12 chains. Longest chain 13 peptides. Score 0.477 Round 4: 86 peptides, 13 chains. Longest chain 12 peptides. Score 0.434 Round 5: 90 peptides, 14 chains. Longest chain 12 peptides. Score 0.431 Taking the results from Round 3 Chains 12, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2522 restraints for refining 1142 atoms. 2230 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3343 (Rfree = 0.000) for 1142 atoms. Found 4 (5 requested) and removed 16 (2 requested) atoms. Cycle 7: After refmac, R = 0.3556 (Rfree = 0.000) for 1110 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 8: After refmac, R = 0.3099 (Rfree = 0.000) for 1094 atoms. Found 3 (5 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.3024 (Rfree = 0.000) for 1080 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 10: After refmac, R = 0.3002 (Rfree = 0.000) for 1064 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.54 4.19 Search for helices and strands: 0 residues in 0 chains, 1132 seeds are put forward NCS extension: 0 residues added, 1132 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.305 Round 2: 81 peptides, 11 chains. Longest chain 14 peptides. Score 0.461 Round 3: 83 peptides, 10 chains. Longest chain 17 peptides. Score 0.503 Round 4: 81 peptides, 11 chains. Longest chain 10 peptides. Score 0.461 Round 5: 94 peptides, 13 chains. Longest chain 13 peptides. Score 0.486 Taking the results from Round 3 Chains 10, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2438 restraints for refining 1112 atoms. 2156 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3028 (Rfree = 0.000) for 1112 atoms. Found 4 (5 requested) and removed 15 (2 requested) atoms. Cycle 12: After refmac, R = 0.2857 (Rfree = 0.000) for 1085 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. Cycle 13: After refmac, R = 0.2973 (Rfree = 0.000) for 1067 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 14: After refmac, R = 0.3215 (Rfree = 0.000) for 1046 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.3409 (Rfree = 0.000) for 1026 atoms. Found 4 (4 requested) and removed 71 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.12 3.80 Search for helices and strands: 0 residues in 0 chains, 1022 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1047 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.319 Round 2: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.374 Round 3: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.374 Round 4: 74 peptides, 11 chains. Longest chain 9 peptides. Score 0.413 Round 5: 74 peptides, 10 chains. Longest chain 14 peptides. Score 0.445 Taking the results from Round 5 Chains 10, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2599 restraints for refining 1173 atoms. 2353 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.4190 (Rfree = 0.000) for 1173 atoms. Found 5 (5 requested) and removed 48 (2 requested) atoms. Cycle 17: After refmac, R = 0.3546 (Rfree = 0.000) for 1117 atoms. Found 4 (5 requested) and removed 30 (2 requested) atoms. Cycle 18: After refmac, R = 0.3462 (Rfree = 0.000) for 1073 atoms. Found 3 (5 requested) and removed 17 (2 requested) atoms. Cycle 19: After refmac, R = 0.3528 (Rfree = 0.000) for 1047 atoms. Found 2 (5 requested) and removed 17 (2 requested) atoms. Cycle 20: After refmac, R = 0.3237 (Rfree = 0.000) for 1023 atoms. Found 1 (4 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 5.10 4.71 Search for helices and strands: 0 residues in 0 chains, 1073 seeds are put forward NCS extension: 0 residues added, 1073 seeds are put forward Round 1: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.349 Round 2: 76 peptides, 11 chains. Longest chain 10 peptides. Score 0.427 Round 3: 78 peptides, 10 chains. Longest chain 17 peptides. Score 0.471 Round 4: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.403 Round 5: 79 peptides, 11 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 3 Chains 10, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2529 restraints for refining 1113 atoms. 2267 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3538 (Rfree = 0.000) for 1113 atoms. Found 2 (5 requested) and removed 11 (2 requested) atoms. Cycle 22: After refmac, R = 0.3056 (Rfree = 0.000) for 1089 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 23: After refmac, R = 0.3101 (Rfree = 0.000) for 1077 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.3155 (Rfree = 0.000) for 1068 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 25: After refmac, R = 0.3046 (Rfree = 0.000) for 1052 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 5.10 4.71 Search for helices and strands: 0 residues in 0 chains, 1096 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1123 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 11 peptides. Score 0.332 Round 2: 75 peptides, 10 chains. Longest chain 15 peptides. Score 0.451 Round 3: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.403 Round 4: 79 peptides, 12 chains. Longest chain 15 peptides. Score 0.417 Round 5: 69 peptides, 10 chains. Longest chain 15 peptides. Score 0.410 Taking the results from Round 2 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2130 restraints for refining 1065 atoms. 1846 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3256 (Rfree = 0.000) for 1065 atoms. Found 2 (5 requested) and removed 11 (2 requested) atoms. Cycle 27: After refmac, R = 0.3172 (Rfree = 0.000) for 1047 atoms. Found 2 (5 requested) and removed 12 (2 requested) atoms. Cycle 28: After refmac, R = 0.3134 (Rfree = 0.000) for 1025 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.3176 (Rfree = 0.000) for 1012 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.3123 (Rfree = 0.000) for 1006 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.13 3.81 Search for helices and strands: 0 residues in 0 chains, 1060 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 1064 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.263 Round 2: 69 peptides, 10 chains. Longest chain 14 peptides. Score 0.410 Round 3: 80 peptides, 11 chains. Longest chain 11 peptides. Score 0.454 Round 4: 79 peptides, 10 chains. Longest chain 17 peptides. Score 0.478 Round 5: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 4 Chains 10, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2343 restraints for refining 1065 atoms. 2077 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3391 (Rfree = 0.000) for 1065 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 32: After refmac, R = 0.3285 (Rfree = 0.000) for 1046 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.3072 (Rfree = 0.000) for 1044 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 34: After refmac, R = 0.3250 (Rfree = 0.000) for 1028 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 35: After refmac, R = 0.3128 (Rfree = 0.000) for 1016 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.14 3.82 Search for helices and strands: 0 residues in 0 chains, 1066 seeds are put forward NCS extension: 0 residues added, 1066 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.263 Round 2: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.326 Round 3: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.356 Round 4: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.430 Round 5: 76 peptides, 12 chains. Longest chain 9 peptides. Score 0.396 Taking the results from Round 4 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2372 restraints for refining 1108 atoms. 2108 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3366 (Rfree = 0.000) for 1108 atoms. Found 5 (5 requested) and removed 16 (2 requested) atoms. Cycle 37: After refmac, R = 0.3231 (Rfree = 0.000) for 1084 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 38: After refmac, R = 0.3020 (Rfree = 0.000) for 1069 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 39: After refmac, R = 0.3008 (Rfree = 0.000) for 1059 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2906 (Rfree = 0.000) for 1055 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.10 3.78 Search for helices and strands: 0 residues in 0 chains, 1124 seeds are put forward NCS extension: 0 residues added, 1124 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.289 Round 2: 68 peptides, 10 chains. Longest chain 12 peptides. Score 0.403 Round 3: 72 peptides, 10 chains. Longest chain 13 peptides. Score 0.431 Round 4: 72 peptides, 12 chains. Longest chain 9 peptides. Score 0.367 Round 5: 65 peptides, 10 chains. Longest chain 15 peptides. Score 0.381 Taking the results from Round 3 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2299 reflections ( 99.14 % complete ) and 2471 restraints for refining 1130 atoms. 2233 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3255 (Rfree = 0.000) for 1130 atoms. Found 5 (5 requested) and removed 24 (2 requested) atoms. Cycle 42: After refmac, R = 0.3225 (Rfree = 0.000) for 1101 atoms. Found 4 (5 requested) and removed 13 (2 requested) atoms. Cycle 43: After refmac, R = 0.3176 (Rfree = 0.000) for 1083 atoms. Found 4 (5 requested) and removed 12 (2 requested) atoms. Cycle 44: After refmac, R = 0.2909 (Rfree = 0.000) for 1071 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 45: After refmac, R = 0.2849 (Rfree = 0.000) for 1061 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.01 3.70 Search for helices and strands: 0 residues in 0 chains, 1097 seeds are put forward NCS extension: 0 residues added, 1097 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 9 peptides. Score 0.231 Round 2: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.340 Round 3: 66 peptides, 10 chains. Longest chain 12 peptides. Score 0.388 Round 4: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.352 Round 5: 71 peptides, 10 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 61, 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 2obp-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2299 reflections ( 99.14 % complete ) and 2375 restraints for refining 1090 atoms. 2141 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3085 (Rfree = 0.000) for 1090 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3001 (Rfree = 0.000) for 1084 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2894 (Rfree = 0.000) for 1075 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2906 (Rfree = 0.000) for 1066 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:18 GMT 2018 Job finished. TimeTaking 30.27 Used memory is bytes: 21502176