Sun 23 Dec 22:23:05 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 2pv4-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.2-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/2pv4-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.2-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 ============================================================ Sun 23 Dec 22:23:14 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/2pv4-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.2-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 112 and 0 Target number of residues in the AU: 112 Target solvent content: 0.6388 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 145 Adjusted target solvent content: 0.53 Input MTZ file: 2pv4-3.2-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: 35.957 47.283 98.695 90.000 90.000 90.000 Input sequence file: 2pv4-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1160 target number of atoms Had to go as low as 0.70 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: 49.347 3.200 Wilson plot Bfac: 71.28 3033 reflections ( 99.54 % complete ) and 0 restraints for refining 1289 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3326 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3248 (Rfree = 0.000) for 1289 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 1330 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.266 Round 2: 86 peptides, 14 chains. Longest chain 11 peptides. Score 0.469 Round 3: 93 peptides, 14 chains. Longest chain 12 peptides. Score 0.527 Round 4: 99 peptides, 10 chains. Longest chain 22 peptides. Score 0.692 Round 5: 101 peptides, 13 chains. Longest chain 15 peptides. Score 0.619 Taking the results from Round 4 Chains 10, Residues 89, Estimated correctness of the model 63.5 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 1985 restraints for refining 1053 atoms. 1554 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3270 (Rfree = 0.000) for 1053 atoms. Found 9 (9 requested) and removed 32 (4 requested) atoms. Cycle 2: After refmac, R = 0.3038 (Rfree = 0.000) for 1008 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2904 (Rfree = 0.000) for 1000 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.2778 (Rfree = 0.000) for 989 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.2841 (Rfree = 0.000) for 980 atoms. Found 4 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 1022 seeds are put forward Round 1: 96 peptides, 13 chains. Longest chain 19 peptides. Score 0.584 Round 2: 89 peptides, 10 chains. Longest chain 16 peptides. Score 0.630 Round 3: 95 peptides, 14 chains. Longest chain 14 peptides. Score 0.543 Round 4: 89 peptides, 12 chains. Longest chain 20 peptides. Score 0.565 Round 5: 91 peptides, 11 chains. Longest chain 12 peptides. Score 0.612 Taking the results from Round 2 Chains 10, Residues 79, Estimated correctness of the model 48.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 1981 restraints for refining 946 atoms. 1675 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2837 (Rfree = 0.000) for 946 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2750 (Rfree = 0.000) for 947 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2450 (Rfree = 0.000) for 947 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2519 (Rfree = 0.000) for 944 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2092 (Rfree = 0.000) for 940 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 1006 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 10 peptides. Score 0.490 Round 2: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.409 Round 3: 99 peptides, 15 chains. Longest chain 16 peptides. Score 0.540 Round 4: 107 peptides, 14 chains. Longest chain 16 peptides. Score 0.629 Round 5: 96 peptides, 12 chains. Longest chain 14 peptides. Score 0.615 Taking the results from Round 4 Chains 16, Residues 93, Estimated correctness of the model 48.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 2013 restraints for refining 1041 atoms. 1627 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2843 (Rfree = 0.000) for 1041 atoms. Found 8 (9 requested) and removed 19 (4 requested) atoms. Cycle 12: After refmac, R = 0.2689 (Rfree = 0.000) for 1020 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2347 (Rfree = 0.000) for 1007 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2178 (Rfree = 0.000) for 1005 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2284 (Rfree = 0.000) for 1002 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 1081 seeds are put forward Round 1: 75 peptides, 12 chains. Longest chain 10 peptides. Score 0.449 Round 2: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.475 Round 3: 83 peptides, 12 chains. Longest chain 13 peptides. Score 0.517 Round 4: 82 peptides, 11 chains. Longest chain 11 peptides. Score 0.545 Round 5: 77 peptides, 9 chains. Longest chain 13 peptides. Score 0.577 Taking the results from Round 5 Chains 9, Residues 68, Estimated correctness of the model 34.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 2071 restraints for refining 1034 atoms. 1765 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2802 (Rfree = 0.000) for 1034 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 17: After refmac, R = 0.2438 (Rfree = 0.000) for 1026 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.2569 (Rfree = 0.000) for 1024 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 19: After refmac, R = 0.2614 (Rfree = 0.000) for 1016 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2037 (Rfree = 0.000) for 1011 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 1071 seeds are put forward Round 1: 82 peptides, 12 chains. Longest chain 13 peptides. Score 0.509 Round 2: 92 peptides, 12 chains. Longest chain 14 peptides. Score 0.587 Round 3: 91 peptides, 12 chains. Longest chain 16 peptides. Score 0.580 Round 4: 89 peptides, 12 chains. Longest chain 16 peptides. Score 0.565 Round 5: 87 peptides, 9 chains. Longest chain 20 peptides. Score 0.647 Taking the results from Round 5 Chains 9, Residues 78, Estimated correctness of the model 53.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 2191 restraints for refining 1035 atoms. 1888 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2511 (Rfree = 0.000) for 1035 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 22: After refmac, R = 0.2371 (Rfree = 0.000) for 1036 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2322 (Rfree = 0.000) for 1033 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2352 (Rfree = 0.000) for 1031 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2276 (Rfree = 0.000) for 1031 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.21 Search for helices and strands: 0 residues in 0 chains, 1083 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.402 Round 2: 102 peptides, 15 chains. Longest chain 12 peptides. Score 0.563 Round 3: 98 peptides, 12 chains. Longest chain 19 peptides. Score 0.629 Round 4: 99 peptides, 13 chains. Longest chain 18 peptides. Score 0.605 Round 5: 90 peptides, 12 chains. Longest chain 12 peptides. Score 0.572 Taking the results from Round 3 Chains 12, Residues 86, Estimated correctness of the model 48.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 2303 restraints for refining 1059 atoms. 1971 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3241 (Rfree = 0.000) for 1059 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 27: After refmac, R = 0.2702 (Rfree = 0.000) for 1048 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.2428 (Rfree = 0.000) for 1041 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.2670 (Rfree = 0.000) for 1038 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2229 (Rfree = 0.000) for 1040 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 1088 seeds are put forward Round 1: 76 peptides, 9 chains. Longest chain 25 peptides. Score 0.569 Round 2: 87 peptides, 10 chains. Longest chain 17 peptides. Score 0.616 Round 3: 89 peptides, 14 chains. Longest chain 9 peptides. Score 0.495 Round 4: 90 peptides, 11 chains. Longest chain 17 peptides. Score 0.605 Round 5: 86 peptides, 11 chains. Longest chain 18 peptides. Score 0.576 Taking the results from Round 2 Chains 10, Residues 77, Estimated correctness of the model 45.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 2147 restraints for refining 1033 atoms. 1849 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2332 (Rfree = 0.000) for 1033 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2677 (Rfree = 0.000) for 1032 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2443 (Rfree = 0.000) for 1035 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.2589 (Rfree = 0.000) for 1036 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2534 (Rfree = 0.000) for 1034 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 1094 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 12 peptides. Score 0.363 Round 2: 92 peptides, 13 chains. Longest chain 20 peptides. Score 0.554 Round 3: 86 peptides, 14 chains. Longest chain 9 peptides. Score 0.469 Round 4: 75 peptides, 11 chains. Longest chain 13 peptides. Score 0.487 Round 5: 76 peptides, 12 chains. Longest chain 8 peptides. Score 0.458 Taking the results from Round 2 Chains 13, Residues 79, Estimated correctness of the model 28.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 2173 restraints for refining 1059 atoms. 1870 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2278 (Rfree = 0.000) for 1059 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2301 (Rfree = 0.000) for 1053 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.2013 (Rfree = 0.000) for 1051 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1805 (Rfree = 0.000) for 1051 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1932 (Rfree = 0.000) for 1045 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 1118 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 11 peptides. Score 0.351 Round 2: 73 peptides, 12 chains. Longest chain 11 peptides. Score 0.430 Round 3: 77 peptides, 13 chains. Longest chain 11 peptides. Score 0.427 Round 4: 80 peptides, 14 chains. Longest chain 11 peptides. Score 0.416 Round 5: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.446 Taking the results from Round 5 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3033 reflections ( 99.54 % complete ) and 2332 restraints for refining 1059 atoms. 2081 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2241 (Rfree = 0.000) for 1059 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2081 (Rfree = 0.000) for 1057 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2025 (Rfree = 0.000) for 1053 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2002 (Rfree = 0.000) for 1054 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2172 (Rfree = 0.000) for 1049 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 1092 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 10 peptides. Score 0.341 Round 2: 73 peptides, 12 chains. Longest chain 11 peptides. Score 0.430 Round 3: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.467 Round 4: 73 peptides, 11 chains. Longest chain 12 peptides. Score 0.470 Round 5: 66 peptides, 10 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 62, Estimated correctness of the model 1.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pv4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3033 reflections ( 99.54 % complete ) and 2344 restraints for refining 1059 atoms. 2107 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2436 (Rfree = 0.000) for 1059 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2285 (Rfree = 0.000) for 1053 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2287 (Rfree = 0.000) for 1049 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2202 (Rfree = 0.000) for 1044 atoms. TimeTaking 24.17