Sun 23 Dec 22:22:59 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 2i9w-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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/2i9w-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 22:23:08 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/2i9w-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 117 and 0 Target number of residues in the AU: 117 Target solvent content: 0.6664 Checking the provided sequence file Detected sequence length: 184 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 184 Adjusted target solvent content: 0.48 Input MTZ file: 2i9w-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: 19 Cell parameters: 41.450 54.640 83.800 90.000 90.000 90.000 Input sequence file: 2i9w-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1472 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 Loops will be built when appropriate and at the last cycle Resolution range: 45.770 4.000 Wilson plot Bfac: 87.71 1784 reflections ( 99.39 % complete ) and 0 restraints for refining 1636 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3723 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3260 (Rfree = 0.000) for 1636 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 1653 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.257 Round 2: 52 peptides, 10 chains. Longest chain 11 peptides. Score 0.295 Round 3: 61 peptides, 10 chains. Longest chain 10 peptides. Score 0.379 Round 4: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.330 Round 5: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.411 Taking the results from Round 5 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 3352 restraints for refining 1330 atoms. 3131 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2817 (Rfree = 0.000) for 1330 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 2: After refmac, R = 0.2707 (Rfree = 0.000) for 1316 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.2534 (Rfree = 0.000) for 1305 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 4: After refmac, R = 0.2667 (Rfree = 0.000) for 1299 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2417 (Rfree = 0.000) for 1297 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 10 peptides. Score 0.251 Round 2: 68 peptides, 11 chains. Longest chain 10 peptides. Score 0.402 Round 3: 65 peptides, 10 chains. Longest chain 16 peptides. Score 0.414 Round 4: 65 peptides, 10 chains. Longest chain 19 peptides. Score 0.414 Round 5: 75 peptides, 11 chains. Longest chain 23 peptides. Score 0.460 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 3019 restraints for refining 1234 atoms. 2774 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2658 (Rfree = 0.000) for 1234 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 7: After refmac, R = 0.2644 (Rfree = 0.000) for 1220 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 8: After refmac, R = 0.2305 (Rfree = 0.000) for 1209 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.2236 (Rfree = 0.000) for 1206 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 10: After refmac, R = 0.2177 (Rfree = 0.000) for 1197 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 1219 seeds are put forward Round 1: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.308 Round 2: 67 peptides, 9 chains. Longest chain 24 peptides. Score 0.468 Round 3: 70 peptides, 11 chains. Longest chain 11 peptides. Score 0.419 Round 4: 69 peptides, 11 chains. Longest chain 12 peptides. Score 0.411 Round 5: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 2 Chains 9, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 2798 restraints for refining 1156 atoms. 2575 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2468 (Rfree = 0.000) for 1156 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 12: After refmac, R = 0.2759 (Rfree = 0.000) for 1148 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 13: After refmac, R = 0.2589 (Rfree = 0.000) for 1137 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.2505 (Rfree = 0.000) for 1127 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2340 (Rfree = 0.000) for 1122 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 1151 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.219 Round 2: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.330 Round 3: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.335 Round 4: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.390 Round 5: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.437 Taking the results from Round 5 Chains 13, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 2608 restraints for refining 1128 atoms. 2349 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2457 (Rfree = 0.000) for 1128 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 17: After refmac, R = 0.2313 (Rfree = 0.000) for 1113 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.2394 (Rfree = 0.000) for 1111 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.2184 (Rfree = 0.000) for 1100 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2205 (Rfree = 0.000) for 1096 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 1146 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.249 Round 2: 75 peptides, 13 chains. Longest chain 16 peptides. Score 0.387 Round 3: 77 peptides, 13 chains. Longest chain 10 peptides. Score 0.404 Round 4: 82 peptides, 13 chains. Longest chain 12 peptides. Score 0.445 Round 5: 82 peptides, 13 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 5 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 2637 restraints for refining 1167 atoms. 2374 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2526 (Rfree = 0.000) for 1167 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 22: After refmac, R = 0.2753 (Rfree = 0.000) for 1153 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2626 (Rfree = 0.000) for 1148 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 24: After refmac, R = 0.2879 (Rfree = 0.000) for 1141 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 25: After refmac, R = 0.2613 (Rfree = 0.000) for 1137 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 1193 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 16 peptides. Score 0.361 Round 2: 67 peptides, 11 chains. Longest chain 15 peptides. Score 0.393 Round 3: 64 peptides, 9 chains. Longest chain 17 peptides. Score 0.444 Round 4: 67 peptides, 10 chains. Longest chain 18 peptides. Score 0.431 Round 5: 61 peptides, 9 chains. Longest chain 19 peptides. Score 0.418 Taking the results from Round 3 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 2476 restraints for refining 1108 atoms. 2265 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2791 (Rfree = 0.000) for 1108 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 27: After refmac, R = 0.2564 (Rfree = 0.000) for 1101 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2671 (Rfree = 0.000) for 1098 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2680 (Rfree = 0.000) for 1094 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 30: After refmac, R = 0.2324 (Rfree = 0.000) for 1089 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 1125 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 11 peptides. Score 0.252 Round 2: 59 peptides, 12 chains. Longest chain 9 peptides. Score 0.280 Round 3: 57 peptides, 9 chains. Longest chain 18 peptides. Score 0.383 Round 4: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.299 Round 5: 58 peptides, 7 chains. Longest chain 19 peptides. Score 0.471 Taking the results from Round 5 Chains 8, Residues 51, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 2247 restraints for refining 1108 atoms. 1991 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2703 (Rfree = 0.000) for 1108 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 32: After refmac, R = 0.2129 (Rfree = 0.000) for 1095 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2158 (Rfree = 0.000) for 1091 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2095 (Rfree = 0.000) for 1089 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.2708 (Rfree = 0.000) for 1087 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 1111 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.200 Round 2: 51 peptides, 10 chains. Longest chain 12 peptides. Score 0.285 Round 3: 56 peptides, 10 chains. Longest chain 12 peptides. Score 0.333 Round 4: 55 peptides, 10 chains. Longest chain 10 peptides. Score 0.324 Round 5: 64 peptides, 12 chains. Longest chain 13 peptides. Score 0.328 Taking the results from Round 3 Chains 10, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 2467 restraints for refining 1071 atoms. 2293 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2483 (Rfree = 0.000) for 1071 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.2335 (Rfree = 0.000) for 1065 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.2588 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.2259 (Rfree = 0.000) for 1060 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 40: After refmac, R = 0.2603 (Rfree = 0.000) for 1053 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 1090 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 8 peptides. Score 0.221 Round 2: 58 peptides, 9 chains. Longest chain 17 peptides. Score 0.392 Round 3: 61 peptides, 11 chains. Longest chain 15 peptides. Score 0.340 Round 4: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.312 Round 5: 61 peptides, 10 chains. Longest chain 17 peptides. Score 0.379 Taking the results from Round 2 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1784 reflections ( 99.39 % complete ) and 2187 restraints for refining 1021 atoms. 2000 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2357 (Rfree = 0.000) for 1021 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 42: After refmac, R = 0.2188 (Rfree = 0.000) for 1016 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.2524 (Rfree = 0.000) for 1013 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2417 (Rfree = 0.000) for 1011 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2358 (Rfree = 0.000) for 1007 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 1051 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.236 Round 2: 49 peptides, 10 chains. Longest chain 9 peptides. Score 0.265 Round 3: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.288 Round 4: 51 peptides, 9 chains. Longest chain 12 peptides. Score 0.328 Round 5: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.275 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 42, 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 2i9w-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1784 reflections ( 99.39 % complete ) and 2266 restraints for refining 1020 atoms. 2107 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2494 (Rfree = 0.000) for 1020 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2341 (Rfree = 0.000) for 1015 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2343 (Rfree = 0.000) for 1011 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2305 (Rfree = 0.000) for 1009 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... TimeTaking 24.08