Sun 23 Dec 22:22:49 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 1vr8-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.6-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/1vr8-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.6-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 22:22:59 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/1vr8-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.6-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: 0.6168 Checking the provided sequence file Detected sequence length: 142 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 142 Adjusted target solvent content: 0.55 Input MTZ file: 1vr8-3.6-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: 154 Cell parameters: 57.762 57.762 87.976 90.000 90.000 120.000 Input sequence file: 1vr8-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1136 target number of atoms Had to go as low as 0.85 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: 50.023 3.601 Wilson plot Bfac: 59.55 2147 reflections ( 99.72 % complete ) and 0 restraints for refining 1272 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3396 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3372 (Rfree = 0.000) for 1272 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 1292 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.321 Round 2: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.478 Round 3: 85 peptides, 12 chains. Longest chain 18 peptides. Score 0.530 Round 4: 77 peptides, 11 chains. Longest chain 17 peptides. Score 0.501 Round 5: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.546 Taking the results from Round 5 Chains 12, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2307 restraints for refining 1030 atoms. 2019 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2667 (Rfree = 0.000) for 1030 atoms. Found 4 (6 requested) and removed 11 (3 requested) atoms. Cycle 2: After refmac, R = 0.2409 (Rfree = 0.000) for 1014 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 1005 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2166 (Rfree = 0.000) for 994 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2091 (Rfree = 0.000) for 985 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 1017 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 10 peptides. Score 0.343 Round 2: 85 peptides, 12 chains. Longest chain 17 peptides. Score 0.530 Round 3: 88 peptides, 11 chains. Longest chain 22 peptides. Score 0.587 Round 4: 92 peptides, 13 chains. Longest chain 14 peptides. Score 0.551 Round 5: 89 peptides, 11 chains. Longest chain 17 peptides. Score 0.594 Taking the results from Round 5 Chains 11, Residues 78, Estimated correctness of the model 12.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2363 restraints for refining 1030 atoms. 2062 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2521 (Rfree = 0.000) for 1030 atoms. Found 3 (6 requested) and removed 10 (3 requested) atoms. Cycle 7: After refmac, R = 0.2281 (Rfree = 0.000) for 1010 atoms. Found 5 (6 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.2146 (Rfree = 0.000) for 995 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2107 (Rfree = 0.000) for 992 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2154 (Rfree = 0.000) for 988 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 1027 seeds are put forward Round 1: 74 peptides, 13 chains. Longest chain 12 peptides. Score 0.397 Round 2: 86 peptides, 10 chains. Longest chain 17 peptides. Score 0.605 Round 3: 90 peptides, 12 chains. Longest chain 20 peptides. Score 0.569 Round 4: 90 peptides, 12 chains. Longest chain 17 peptides. Score 0.569 Round 5: 88 peptides, 13 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 2 Chains 10, Residues 76, Estimated correctness of the model 16.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2270 restraints for refining 1026 atoms. 1976 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2309 (Rfree = 0.000) for 1026 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 12: After refmac, R = 0.2044 (Rfree = 0.000) for 1020 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.1956 (Rfree = 0.000) for 1018 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.1947 (Rfree = 0.000) for 1014 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1928 (Rfree = 0.000) for 1013 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 1055 seeds are put forward Round 1: 85 peptides, 15 chains. Longest chain 16 peptides. Score 0.420 Round 2: 83 peptides, 11 chains. Longest chain 17 peptides. Score 0.550 Round 3: 77 peptides, 10 chains. Longest chain 14 peptides. Score 0.538 Round 4: 83 peptides, 10 chains. Longest chain 14 peptides. Score 0.584 Round 5: 88 peptides, 11 chains. Longest chain 22 peptides. Score 0.587 Taking the results from Round 5 Chains 11, Residues 77, Estimated correctness of the model 9.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2276 restraints for refining 1030 atoms. 1979 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2316 (Rfree = 0.000) for 1030 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2391 (Rfree = 0.000) for 1025 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2181 (Rfree = 0.000) for 1025 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2268 (Rfree = 0.000) for 1022 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2143 (Rfree = 0.000) for 1017 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.07 Search for helices and strands: 0 residues in 0 chains, 1054 seeds are put forward Round 1: 79 peptides, 13 chains. Longest chain 10 peptides. Score 0.443 Round 2: 91 peptides, 12 chains. Longest chain 21 peptides. Score 0.576 Round 3: 90 peptides, 12 chains. Longest chain 18 peptides. Score 0.569 Round 4: 95 peptides, 13 chains. Longest chain 14 peptides. Score 0.573 Round 5: 94 peptides, 11 chains. Longest chain 24 peptides. Score 0.629 Taking the results from Round 5 Chains 12, Residues 83, Estimated correctness of the model 25.6 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 1993 restraints for refining 1030 atoms. 1610 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2646 (Rfree = 0.000) for 1030 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 22: After refmac, R = 0.2614 (Rfree = 0.000) for 1000 atoms. Found 5 (6 requested) and removed 20 (3 requested) atoms. Cycle 23: After refmac, R = 0.2644 (Rfree = 0.000) for 972 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2809 (Rfree = 0.000) for 968 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2489 (Rfree = 0.000) for 960 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.06 Search for helices and strands: 0 residues in 0 chains, 989 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 9 peptides. Score 0.319 Round 2: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.311 Round 3: 77 peptides, 12 chains. Longest chain 12 peptides. Score 0.464 Round 4: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.458 Round 5: 77 peptides, 11 chains. Longest chain 12 peptides. Score 0.501 Taking the results from Round 5 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2201 restraints for refining 1029 atoms. 1948 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2874 (Rfree = 0.000) for 1029 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.2661 (Rfree = 0.000) for 1017 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2328 (Rfree = 0.000) for 1009 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2226 (Rfree = 0.000) for 1000 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2555 (Rfree = 0.000) for 997 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 1036 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.309 Round 2: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.419 Round 3: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.443 Round 4: 72 peptides, 12 chains. Longest chain 12 peptides. Score 0.419 Round 5: 71 peptides, 11 chains. Longest chain 14 peptides. Score 0.449 Taking the results from Round 5 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2270 restraints for refining 1004 atoms. 2041 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2396 (Rfree = 0.000) for 1004 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.2499 (Rfree = 0.000) for 999 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.2359 (Rfree = 0.000) for 991 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.2208 (Rfree = 0.000) for 986 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 35: After refmac, R = 0.2232 (Rfree = 0.000) for 980 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 1012 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.258 Round 2: 66 peptides, 12 chains. Longest chain 14 peptides. Score 0.361 Round 3: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.344 Round 4: 66 peptides, 12 chains. Longest chain 11 peptides. Score 0.361 Round 5: 69 peptides, 12 chains. Longest chain 14 peptides. Score 0.391 Taking the results from Round 5 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2324 restraints for refining 1030 atoms. 2108 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2874 (Rfree = 0.000) for 1030 atoms. Found 5 (6 requested) and removed 24 (3 requested) atoms. Cycle 37: After refmac, R = 0.2937 (Rfree = 0.000) for 1002 atoms. Found 3 (6 requested) and removed 33 (3 requested) atoms. Cycle 38: After refmac, R = 0.2933 (Rfree = 0.000) for 963 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 39: After refmac, R = 0.2927 (Rfree = 0.000) for 948 atoms. Found 3 (6 requested) and removed 18 (3 requested) atoms. Cycle 40: After refmac, R = 0.2833 (Rfree = 0.000) for 930 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 962 seeds are put forward Round 1: 50 peptides, 12 chains. Longest chain 5 peptides. Score 0.190 Round 2: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.237 Round 3: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.397 Round 4: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.324 Round 5: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.279 Taking the results from Round 3 Chains 10, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2147 reflections ( 99.72 % complete ) and 2070 restraints for refining 950 atoms. 1876 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3270 (Rfree = 0.000) for 950 atoms. Found 6 (6 requested) and removed 24 (3 requested) atoms. Cycle 42: After refmac, R = 0.3112 (Rfree = 0.000) for 925 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 43: After refmac, R = 0.2774 (Rfree = 0.000) for 913 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.2751 (Rfree = 0.000) for 912 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.3164 (Rfree = 0.000) for 902 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 928 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.216 Round 2: 49 peptides, 9 chains. Longest chain 8 peptides. Score 0.320 Round 3: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.327 Round 4: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.368 Round 5: 57 peptides, 8 chains. Longest chain 9 peptides. Score 0.444 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 49, 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 1vr8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2147 reflections ( 99.72 % complete ) and 2080 restraints for refining 941 atoms. 1892 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2998 (Rfree = 0.000) for 941 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2917 (Rfree = 0.000) for 933 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2884 (Rfree = 0.000) for 924 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2846 (Rfree = 0.000) for 917 atoms. TimeTaking 24.78