Sun 23 Dec 22:23:08 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 1vjf-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-3.8-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/1vjf-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-3.8-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 22:23:17 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/1vjf-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-3.8-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 118 and 0 Target number of residues in the AU: 118 Target solvent content: 0.5940 Checking the provided sequence file Detected sequence length: 180 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 180 Adjusted target solvent content: 0.38 Input MTZ file: 1vjf-3.8-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: 96 Cell parameters: 50.903 50.903 121.411 90.000 90.000 90.000 Input sequence file: 1vjf-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1440 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: 46.944 3.801 Wilson plot Bfac: 49.82 1803 reflections ( 99.67 % complete ) and 0 restraints for refining 1599 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3308 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3111 (Rfree = 0.000) for 1599 atoms. Found 5 (8 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 1621 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 6 peptides. Score 0.208 Round 2: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.288 Round 3: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.411 Round 4: 86 peptides, 15 chains. Longest chain 18 peptides. Score 0.445 Round 5: 82 peptides, 11 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 5 Chains 12, Residues 71, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2940 restraints for refining 1303 atoms. 2640 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3175 (Rfree = 0.000) for 1303 atoms. Found 6 (7 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.2791 (Rfree = 0.000) for 1278 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 3: After refmac, R = 0.2467 (Rfree = 0.000) for 1256 atoms. Found 3 (6 requested) and removed 9 (3 requested) atoms. Cycle 4: After refmac, R = 0.2659 (Rfree = 0.000) for 1246 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 5: After refmac, R = 0.2545 (Rfree = 0.000) for 1235 atoms. Found 3 (6 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 1283 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.284 Round 2: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.445 Round 3: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.416 Round 4: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.428 Round 5: 86 peptides, 13 chains. Longest chain 15 peptides. Score 0.522 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2584 restraints for refining 1210 atoms. 2266 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2547 (Rfree = 0.000) for 1210 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 7: After refmac, R = 0.2367 (Rfree = 0.000) for 1192 atoms. Found 5 (6 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.2285 (Rfree = 0.000) for 1178 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2338 (Rfree = 0.000) for 1173 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 10: After refmac, R = 0.1794 (Rfree = 0.000) for 1166 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 1206 seeds are put forward Round 1: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.373 Round 2: 84 peptides, 14 chains. Longest chain 12 peptides. Score 0.466 Round 3: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.502 Round 4: 81 peptides, 12 chains. Longest chain 12 peptides. Score 0.517 Round 5: 78 peptides, 13 chains. Longest chain 9 peptides. Score 0.450 Taking the results from Round 4 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2644 restraints for refining 1179 atoms. 2364 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2552 (Rfree = 0.000) for 1179 atoms. Found 5 (6 requested) and removed 14 (3 requested) atoms. Cycle 12: After refmac, R = 0.2633 (Rfree = 0.000) for 1163 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 13: After refmac, R = 0.2821 (Rfree = 0.000) for 1150 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2559 (Rfree = 0.000) for 1147 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2647 (Rfree = 0.000) for 1143 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 1195 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.239 Round 2: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.347 Round 3: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.280 Round 4: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.453 Round 5: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.404 Taking the results from Round 4 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2660 restraints for refining 1141 atoms. 2424 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2619 (Rfree = 0.000) for 1141 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2495 (Rfree = 0.000) for 1127 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.2435 (Rfree = 0.000) for 1122 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 19: After refmac, R = 0.2038 (Rfree = 0.000) for 1114 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2047 (Rfree = 0.000) for 1111 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 1160 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 6 peptides. Score 0.262 Round 2: 71 peptides, 12 chains. Longest chain 12 peptides. Score 0.424 Round 3: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.397 Round 4: 74 peptides, 13 chains. Longest chain 15 peptides. Score 0.411 Round 5: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 2 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2429 restraints for refining 1120 atoms. 2170 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2233 (Rfree = 0.000) for 1120 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2008 (Rfree = 0.000) for 1116 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2046 (Rfree = 0.000) for 1111 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.1971 (Rfree = 0.000) for 1107 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2058 (Rfree = 0.000) for 1102 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.92 Search for helices and strands: 0 residues in 0 chains, 1140 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.250 Round 2: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.337 Round 3: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.460 Round 4: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.387 Round 5: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 3 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2418 restraints for refining 1140 atoms. 2131 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2323 (Rfree = 0.000) for 1140 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 27: After refmac, R = 0.2132 (Rfree = 0.000) for 1128 atoms. Found 1 (6 requested) and removed 9 (3 requested) atoms. Cycle 28: After refmac, R = 0.2055 (Rfree = 0.000) for 1120 atoms. Found 0 (6 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2056 (Rfree = 0.000) for 1111 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2289 (Rfree = 0.000) for 1107 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.93 Search for helices and strands: 0 residues in 0 chains, 1145 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.326 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.450 Round 3: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.381 Round 4: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.379 Round 5: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 2 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2431 restraints for refining 1156 atoms. 2138 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2453 (Rfree = 0.000) for 1156 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 32: After refmac, R = 0.2391 (Rfree = 0.000) for 1144 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.2448 (Rfree = 0.000) for 1133 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.2034 (Rfree = 0.000) for 1128 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2242 (Rfree = 0.000) for 1121 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 1150 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 5 peptides. Score 0.208 Round 2: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.291 Round 3: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.291 Round 4: 47 peptides, 9 chains. Longest chain 10 peptides. Score 0.305 Round 5: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.294 Taking the results from Round 4 Chains 9, Residues 38, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2581 restraints for refining 1112 atoms. 2423 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2485 (Rfree = 0.000) for 1112 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 37: After refmac, R = 0.2756 (Rfree = 0.000) for 1108 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2064 (Rfree = 0.000) for 1100 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1908 (Rfree = 0.000) for 1095 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1793 (Rfree = 0.000) for 1095 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.92 Search for helices and strands: 0 residues in 0 chains, 1121 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.210 Round 2: 42 peptides, 10 chains. Longest chain 6 peptides. Score 0.193 Round 3: 58 peptides, 12 chains. Longest chain 6 peptides. Score 0.286 Round 4: 50 peptides, 9 chains. Longest chain 8 peptides. Score 0.340 Round 5: 48 peptides, 9 chains. Longest chain 7 peptides. Score 0.317 Taking the results from Round 4 Chains 9, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1803 reflections ( 99.67 % complete ) and 2386 restraints for refining 1037 atoms. 2231 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2522 (Rfree = 0.000) for 1037 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 42: After refmac, R = 0.2635 (Rfree = 0.000) for 1031 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2315 (Rfree = 0.000) for 1028 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2378 (Rfree = 0.000) for 1027 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2234 (Rfree = 0.000) for 1027 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 1065 seeds are put forward Round 1: 26 peptides, 5 chains. Longest chain 7 peptides. Score 0.260 Round 2: 38 peptides, 8 chains. Longest chain 8 peptides. Score 0.248 Round 3: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.273 Round 4: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.260 Round 5: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.301 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 31, 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 1vjf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1803 reflections ( 99.67 % complete ) and 2081 restraints for refining 951 atoms. 1964 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2929 (Rfree = 0.000) for 951 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2660 (Rfree = 0.000) for 948 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2392 (Rfree = 0.000) for 946 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2696 (Rfree = 0.000) for 942 atoms. TimeTaking 24.67