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 2hti-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-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/2hti-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-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 22:23:08 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/2hti-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-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 120 and 0 Target number of residues in the AU: 120 Target solvent content: 0.6657 Checking the provided sequence file Detected sequence length: 185 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 185 Adjusted target solvent content: 0.48 Input MTZ file: 2hti-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: 178 Cell parameters: 72.007 72.007 129.790 90.000 90.000 120.000 Input sequence file: 2hti-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1480 target number of atoms Had to go as low as 0.45 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: 28.784 3.801 Wilson plot Bfac: 88.64 2213 reflections ( 99.24 % complete ) and 0 restraints for refining 1634 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3428 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3812 (Rfree = 0.000) for 1634 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 1648 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.319 Round 2: 77 peptides, 11 chains. Longest chain 12 peptides. Score 0.471 Round 3: 77 peptides, 8 chains. Longest chain 16 peptides. Score 0.571 Round 4: 77 peptides, 9 chains. Longest chain 12 peptides. Score 0.538 Round 5: 74 peptides, 7 chains. Longest chain 16 peptides. Score 0.583 Taking the results from Round 5 Chains 7, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2742 restraints for refining 1130 atoms. 2481 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3165 (Rfree = 0.000) for 1130 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 2: After refmac, R = 0.3016 (Rfree = 0.000) for 1090 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.2912 (Rfree = 0.000) for 1073 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 4: After refmac, R = 0.2780 (Rfree = 0.000) for 1050 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 5: After refmac, R = 0.2666 (Rfree = 0.000) for 1038 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 1074 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 13 peptides. Score 0.358 Round 2: 76 peptides, 11 chains. Longest chain 10 peptides. Score 0.463 Round 3: 74 peptides, 9 chains. Longest chain 14 peptides. Score 0.517 Round 4: 83 peptides, 11 chains. Longest chain 13 peptides. Score 0.516 Round 5: 91 peptides, 11 chains. Longest chain 19 peptides. Score 0.571 Taking the results from Round 5 Chains 11, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2297 restraints for refining 1013 atoms. 1988 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2878 (Rfree = 0.000) for 1013 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 7: After refmac, R = 0.2610 (Rfree = 0.000) for 1001 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 8: After refmac, R = 0.2728 (Rfree = 0.000) for 993 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.2441 (Rfree = 0.000) for 980 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 10: After refmac, R = 0.2580 (Rfree = 0.000) for 974 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 1035 seeds are put forward Round 1: 79 peptides, 13 chains. Longest chain 13 peptides. Score 0.417 Round 2: 77 peptides, 10 chains. Longest chain 15 peptides. Score 0.505 Round 3: 86 peptides, 11 chains. Longest chain 15 peptides. Score 0.537 Round 4: 96 peptides, 14 chains. Longest chain 13 peptides. Score 0.513 Round 5: 87 peptides, 10 chains. Longest chain 16 peptides. Score 0.575 Taking the results from Round 5 Chains 10, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2268 restraints for refining 1028 atoms. 1970 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2834 (Rfree = 0.000) for 1028 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 12: After refmac, R = 0.2772 (Rfree = 0.000) for 1007 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 13: After refmac, R = 0.2754 (Rfree = 0.000) for 999 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 14: After refmac, R = 0.2528 (Rfree = 0.000) for 993 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.2617 (Rfree = 0.000) for 985 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 1039 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.303 Round 2: 80 peptides, 12 chains. Longest chain 11 peptides. Score 0.460 Round 3: 75 peptides, 9 chains. Longest chain 20 peptides. Score 0.524 Round 4: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.415 Round 5: 86 peptides, 13 chains. Longest chain 11 peptides. Score 0.472 Taking the results from Round 3 Chains 9, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2354 restraints for refining 1024 atoms. 2099 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2747 (Rfree = 0.000) for 1024 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 17: After refmac, R = 0.2709 (Rfree = 0.000) for 1003 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2814 (Rfree = 0.000) for 987 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 19: After refmac, R = 0.2640 (Rfree = 0.000) for 975 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 20: After refmac, R = 0.2729 (Rfree = 0.000) for 970 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 1019 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.346 Round 2: 77 peptides, 11 chains. Longest chain 17 peptides. Score 0.471 Round 3: 80 peptides, 9 chains. Longest chain 20 peptides. Score 0.559 Round 4: 82 peptides, 8 chains. Longest chain 18 peptides. Score 0.603 Round 5: 78 peptides, 8 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 4 Chains 8, Residues 74, Estimated correctness of the model 0.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2210 restraints for refining 1026 atoms. 1922 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2779 (Rfree = 0.000) for 1026 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 22: After refmac, R = 0.2664 (Rfree = 0.000) for 1015 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.2471 (Rfree = 0.000) for 1011 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2535 (Rfree = 0.000) for 1005 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.2476 (Rfree = 0.000) for 1000 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 1042 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.329 Round 2: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.431 Round 3: 76 peptides, 11 chains. Longest chain 11 peptides. Score 0.463 Round 4: 74 peptides, 9 chains. Longest chain 16 peptides. Score 0.517 Round 5: 69 peptides, 8 chains. Longest chain 15 peptides. Score 0.514 Taking the results from Round 4 Chains 9, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2403 restraints for refining 1062 atoms. 2152 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2728 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 27: After refmac, R = 0.2625 (Rfree = 0.000) for 1057 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2526 (Rfree = 0.000) for 1055 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2473 (Rfree = 0.000) for 1053 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2452 (Rfree = 0.000) for 1051 atoms. Found 1 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 1084 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 7 peptides. Score 0.349 Round 2: 70 peptides, 11 chains. Longest chain 9 peptides. Score 0.415 Round 3: 73 peptides, 11 chains. Longest chain 16 peptides. Score 0.439 Round 4: 75 peptides, 11 chains. Longest chain 16 peptides. Score 0.455 Round 5: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.415 Taking the results from Round 4 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2403 restraints for refining 1071 atoms. 2158 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2613 (Rfree = 0.000) for 1071 atoms. Found 3 (5 requested) and removed 12 (2 requested) atoms. Cycle 32: After refmac, R = 0.2550 (Rfree = 0.000) for 1058 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.2744 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 34: After refmac, R = 0.2636 (Rfree = 0.000) for 1047 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 35: After refmac, R = 0.2610 (Rfree = 0.000) for 1041 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 1091 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.251 Round 2: 61 peptides, 11 chains. Longest chain 13 peptides. Score 0.337 Round 3: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.312 Round 4: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.346 Round 5: 62 peptides, 9 chains. Longest chain 16 peptides. Score 0.423 Taking the results from Round 5 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2472 restraints for refining 1079 atoms. 2269 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2538 (Rfree = 0.000) for 1079 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.2910 (Rfree = 0.000) for 1063 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 38: After refmac, R = 0.3046 (Rfree = 0.000) for 1051 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 39: After refmac, R = 0.2408 (Rfree = 0.000) for 1036 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 40: After refmac, R = 0.2014 (Rfree = 0.000) for 1028 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 1068 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 8 peptides. Score 0.233 Round 2: 73 peptides, 13 chains. Longest chain 14 peptides. Score 0.367 Round 3: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.425 Round 4: 84 peptides, 13 chains. Longest chain 16 peptides. Score 0.457 Round 5: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 4 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2213 reflections ( 99.24 % complete ) and 2169 restraints for refining 1013 atoms. 1898 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2781 (Rfree = 0.000) for 1013 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 42: After refmac, R = 0.2755 (Rfree = 0.000) for 1003 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.2716 (Rfree = 0.000) for 998 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.2469 (Rfree = 0.000) for 989 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 45: After refmac, R = 0.2481 (Rfree = 0.000) for 981 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 1036 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.249 Round 2: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.361 Round 3: 75 peptides, 11 chains. Longest chain 12 peptides. Score 0.455 Round 4: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.381 Round 5: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 64, 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 2hti-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2213 reflections ( 99.24 % complete ) and 2187 restraints for refining 997 atoms. 1942 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2491 (Rfree = 0.000) for 997 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2274 (Rfree = 0.000) for 992 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2217 (Rfree = 0.000) for 990 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2215 (Rfree = 0.000) for 987 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. TimeTaking 27.2