null Sun 23 Dec 22:23:10 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 2nwv-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nwv-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-1.9-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/2nwv-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-1.9-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 22:23:19 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/2nwv-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nwv-1.9-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 147 and 0 Target number of residues in the AU: 147 Target solvent content: 0.4856 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 114 Adjusted target solvent content: 0.60 Input MTZ file: 2nwv-1.9-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: 179 Cell parameters: 62.452 62.452 137.365 90.000 90.000 120.000 Input sequence file: 2nwv-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 target number of atoms Had to go as low as 0.60 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 1 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: 28.991 1.850 Wilson plot Bfac: 20.04 14235 reflections ( 99.88 % complete ) and 0 restraints for refining 1023 atoms. Observations/parameters ratio is 3.48 ------------------------------------------------------ Starting model: R = 0.3978 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3500 (Rfree = 0.000) for 1023 atoms. Found 38 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.98 1.73 Round 1: 86 peptides, 13 chains. Longest chain 17 peptides. Score 0.526 Round 2: 90 peptides, 7 chains. Longest chain 36 peptides. Score 0.746 Round 3: 95 peptides, 6 chains. Longest chain 32 peptides. Score 0.795 Round 4: 95 peptides, 5 chains. Longest chain 55 peptides. Score 0.817 Round 5: 103 peptides, 4 chains. Longest chain 56 peptides. Score 0.865 Taking the results from Round 5 Chains 4, Residues 99, Estimated correctness of the model 98.6 % 2 chains (70 residues) have been docked in sequence Building loops using Loopy2018 4 chains (99 residues) following loop building 2 chains (70 residues) in sequence following loop building ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1309 restraints for refining 1018 atoms. 579 conditional restraints added. Observations/parameters ratio is 3.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3559 (Rfree = 0.000) for 1018 atoms. Found 43 (43 requested) and removed 30 (21 requested) atoms. Cycle 2: After refmac, R = 0.3228 (Rfree = 0.000) for 1024 atoms. Found 43 (43 requested) and removed 22 (22 requested) atoms. Cycle 3: After refmac, R = 0.3067 (Rfree = 0.000) for 1034 atoms. Found 39 (42 requested) and removed 11 (22 requested) atoms. Cycle 4: After refmac, R = 0.2859 (Rfree = 0.000) for 1055 atoms. Found 31 (43 requested) and removed 15 (22 requested) atoms. Cycle 5: After refmac, R = 0.2716 (Rfree = 0.000) for 1060 atoms. Found 38 (43 requested) and removed 20 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.92 1.68 Round 1: 100 peptides, 3 chains. Longest chain 54 peptides. Score 0.874 Round 2: 101 peptides, 3 chains. Longest chain 54 peptides. Score 0.876 Round 3: 104 peptides, 3 chains. Longest chain 54 peptides. Score 0.885 Round 4: 105 peptides, 2 chains. Longest chain 84 peptides. Score 0.903 Round 5: 107 peptides, 2 chains. Longest chain 86 peptides. Score 0.907 Taking the results from Round 5 Chains 2, Residues 105, Estimated correctness of the model 99.3 % 2 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 29 A 1 chains (109 residues) following loop building 1 chains (109 residues) in sequence following loop building ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1040 restraints for refining 1072 atoms. 101 conditional restraints added. Observations/parameters ratio is 3.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2676 (Rfree = 0.000) for 1072 atoms. Found 40 (42 requested) and removed 27 (22 requested) atoms. Cycle 7: After refmac, R = 0.2453 (Rfree = 0.000) for 1083 atoms. Found 39 (42 requested) and removed 23 (23 requested) atoms. Cycle 8: After refmac, R = 0.2360 (Rfree = 0.000) for 1098 atoms. Found 35 (42 requested) and removed 20 (23 requested) atoms. Cycle 9: After refmac, R = 0.2304 (Rfree = 0.000) for 1109 atoms. Found 27 (41 requested) and removed 17 (23 requested) atoms. Cycle 10: After refmac, R = 0.2215 (Rfree = 0.000) for 1115 atoms. Found 32 (40 requested) and removed 19 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.90 1.66 Round 1: 106 peptides, 2 chains. Longest chain 84 peptides. Score 0.905 Round 2: 107 peptides, 2 chains. Longest chain 84 peptides. Score 0.907 Round 3: 107 peptides, 3 chains. Longest chain 54 peptides. Score 0.892 Round 4: 109 peptides, 2 chains. Longest chain 84 peptides. Score 0.912 Round 5: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Taking the results from Round 5 Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1014 restraints for refining 1072 atoms. 67 conditional restraints added. Observations/parameters ratio is 3.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2249 (Rfree = 0.000) for 1072 atoms. Found 38 (38 requested) and removed 24 (22 requested) atoms. Cycle 12: After refmac, R = 0.2170 (Rfree = 0.000) for 1085 atoms. Found 32 (38 requested) and removed 25 (23 requested) atoms. Cycle 13: After refmac, R = 0.2125 (Rfree = 0.000) for 1092 atoms. Found 34 (37 requested) and removed 23 (23 requested) atoms. Cycle 14: After refmac, R = 0.2110 (Rfree = 0.000) for 1103 atoms. Found 32 (37 requested) and removed 21 (23 requested) atoms. Cycle 15: After refmac, R = 0.2105 (Rfree = 0.000) for 1112 atoms. Found 32 (36 requested) and removed 22 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.90 1.66 Round 1: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 2: 110 peptides, 2 chains. Longest chain 85 peptides. Score 0.914 Round 3: 110 peptides, 2 chains. Longest chain 81 peptides. Score 0.914 Round 4: 110 peptides, 2 chains. Longest chain 56 peptides. Score 0.914 Round 5: 110 peptides, 2 chains. Longest chain 59 peptides. Score 0.914 Taking the results from Round 1 Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1006 restraints for refining 1072 atoms. 59 conditional restraints added. Observations/parameters ratio is 3.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2224 (Rfree = 0.000) for 1072 atoms. Found 32 (33 requested) and removed 24 (22 requested) atoms. Cycle 17: After refmac, R = 0.2121 (Rfree = 0.000) for 1079 atoms. Found 28 (33 requested) and removed 14 (23 requested) atoms. Cycle 18: After refmac, R = 0.2056 (Rfree = 0.000) for 1092 atoms. Found 26 (33 requested) and removed 12 (23 requested) atoms. Cycle 19: After refmac, R = 0.2053 (Rfree = 0.000) for 1104 atoms. Found 23 (34 requested) and removed 13 (23 requested) atoms. Cycle 20: After refmac, R = 0.2025 (Rfree = 0.000) for 1113 atoms. Found 24 (33 requested) and removed 15 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.91 1.67 Round 1: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 2: 110 peptides, 2 chains. Longest chain 83 peptides. Score 0.914 Round 3: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 4: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 5: 110 peptides, 2 chains. Longest chain 81 peptides. Score 0.914 Taking the results from Round 4 Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1016 restraints for refining 1075 atoms. 69 conditional restraints added. Observations/parameters ratio is 3.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2198 (Rfree = 0.000) for 1075 atoms. Found 31 (31 requested) and removed 25 (22 requested) atoms. Cycle 22: After refmac, R = 0.2109 (Rfree = 0.000) for 1080 atoms. Found 30 (30 requested) and removed 11 (23 requested) atoms. Cycle 23: After refmac, R = 0.2090 (Rfree = 0.000) for 1098 atoms. Found 23 (31 requested) and removed 13 (23 requested) atoms. Cycle 24: After refmac, R = 0.2044 (Rfree = 0.000) for 1107 atoms. Found 23 (30 requested) and removed 15 (23 requested) atoms. Cycle 25: After refmac, R = 0.2020 (Rfree = 0.000) for 1115 atoms. Found 23 (29 requested) and removed 15 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.91 1.67 Round 1: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 2: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 3: 110 peptides, 2 chains. Longest chain 81 peptides. Score 0.914 Round 4: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 5: 110 peptides, 2 chains. Longest chain 81 peptides. Score 0.914 Taking the results from Round 4 Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1007 restraints for refining 1072 atoms. 60 conditional restraints added. Observations/parameters ratio is 3.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2213 (Rfree = 0.000) for 1072 atoms. Found 27 (27 requested) and removed 26 (22 requested) atoms. Cycle 27: After refmac, R = 0.2088 (Rfree = 0.000) for 1072 atoms. Found 26 (26 requested) and removed 13 (22 requested) atoms. Cycle 28: After refmac, R = 0.2053 (Rfree = 0.000) for 1083 atoms. Found 27 (27 requested) and removed 11 (23 requested) atoms. Cycle 29: After refmac, R = 0.2034 (Rfree = 0.000) for 1099 atoms. Found 22 (27 requested) and removed 20 (23 requested) atoms. Cycle 30: After refmac, R = 0.2006 (Rfree = 0.000) for 1100 atoms. Found 26 (26 requested) and removed 17 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.91 1.67 Round 1: 108 peptides, 2 chains. Longest chain 84 peptides. Score 0.910 Round 2: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 3: 110 peptides, 2 chains. Longest chain 81 peptides. Score 0.914 Round 4: 108 peptides, 2 chains. Longest chain 84 peptides. Score 0.910 Round 5: 109 peptides, 3 chains. Longest chain 54 peptides. Score 0.897 Taking the results from Round 2 Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1011 restraints for refining 1070 atoms. 64 conditional restraints added. Observations/parameters ratio is 3.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2212 (Rfree = 0.000) for 1070 atoms. Found 24 (24 requested) and removed 24 (22 requested) atoms. Cycle 32: After refmac, R = 0.2090 (Rfree = 0.000) for 1070 atoms. Found 23 (23 requested) and removed 3 (22 requested) atoms. Cycle 33: After refmac, R = 0.2044 (Rfree = 0.000) for 1090 atoms. Found 19 (24 requested) and removed 11 (23 requested) atoms. Cycle 34: After refmac, R = 0.2010 (Rfree = 0.000) for 1097 atoms. Found 23 (23 requested) and removed 7 (23 requested) atoms. Cycle 35: After refmac, R = 0.1993 (Rfree = 0.000) for 1112 atoms. Found 20 (23 requested) and removed 13 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.91 1.67 Round 1: 108 peptides, 2 chains. Longest chain 84 peptides. Score 0.910 Round 2: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 3: 110 peptides, 2 chains. Longest chain 81 peptides. Score 0.914 Round 4: 108 peptides, 2 chains. Longest chain 84 peptides. Score 0.910 Round 5: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Taking the results from Round 5 Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1006 restraints for refining 1071 atoms. 59 conditional restraints added. Observations/parameters ratio is 3.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2194 (Rfree = 0.000) for 1071 atoms. Found 22 (22 requested) and removed 26 (22 requested) atoms. Cycle 37: After refmac, R = 0.2109 (Rfree = 0.000) for 1067 atoms. Found 22 (22 requested) and removed 7 (22 requested) atoms. Cycle 38: After refmac, R = 0.2042 (Rfree = 0.000) for 1081 atoms. Found 23 (23 requested) and removed 10 (23 requested) atoms. Cycle 39: After refmac, R = 0.2027 (Rfree = 0.000) for 1093 atoms. Found 23 (23 requested) and removed 13 (23 requested) atoms. Cycle 40: After refmac, R = 0.2014 (Rfree = 0.000) for 1102 atoms. Found 23 (23 requested) and removed 20 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.91 1.67 Round 1: 108 peptides, 2 chains. Longest chain 84 peptides. Score 0.910 Round 2: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 3: 110 peptides, 2 chains. Longest chain 81 peptides. Score 0.914 Round 4: 110 peptides, 2 chains. Longest chain 56 peptides. Score 0.914 Round 5: 108 peptides, 3 chains. Longest chain 55 peptides. Score 0.895 Taking the results from Round 2 Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14235 reflections ( 99.88 % complete ) and 1006 restraints for refining 1069 atoms. 59 conditional restraints added. Observations/parameters ratio is 3.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2199 (Rfree = 0.000) for 1069 atoms. Found 22 (22 requested) and removed 23 (22 requested) atoms. Cycle 42: After refmac, R = 0.2088 (Rfree = 0.000) for 1067 atoms. Found 22 (22 requested) and removed 4 (22 requested) atoms. Cycle 43: After refmac, R = 0.2033 (Rfree = 0.000) for 1083 atoms. Found 23 (23 requested) and removed 11 (23 requested) atoms. Cycle 44: After refmac, R = 0.2020 (Rfree = 0.000) for 1094 atoms. Found 23 (23 requested) and removed 16 (23 requested) atoms. Cycle 45: After refmac, R = 0.2012 (Rfree = 0.000) for 1101 atoms. Found 23 (23 requested) and removed 14 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.91 1.67 Round 1: 108 peptides, 2 chains. Longest chain 84 peptides. Score 0.910 Round 2: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.929 Round 3: 107 peptides, 3 chains. Longest chain 54 peptides. Score 0.892 Round 4: 108 peptides, 2 chains. Longest chain 84 peptides. Score 0.910 Round 5: 110 peptides, 2 chains. Longest chain 56 peptides. Score 0.914 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 110, Estimated correctness of the model 99.6 % 1 chains (110 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14235 reflections ( 99.88 % complete ) and 947 restraints for refining 926 atoms. Observations/parameters ratio is 3.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2686 (Rfree = 0.000) for 926 atoms. Found 19 (19 requested) and removed 0 (19 requested) atoms. Cycle 47: After refmac, R = 0.2509 (Rfree = 0.000) for 926 atoms. Found 14 (20 requested) and removed 0 (20 requested) atoms. Cycle 48: After refmac, R = 0.2352 (Rfree = 0.000) for 926 atoms. Found 2 (20 requested) and removed 1 (20 requested) atoms. Cycle 49: After refmac, R = 0.2293 (Rfree = 0.000) for 926 atoms. Found 6 (20 requested) and removed 1 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:02 GMT 2018 Job finished. TimeTaking 29.88 Used memory is bytes: 17344672