null 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 2ooc-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-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/2ooc-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-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 22:23:08 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/2ooc-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-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 254 and 0 Target number of residues in the AU: 254 Target solvent content: 0.4729 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.53 Input MTZ file: 2ooc-1.6-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: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 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 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 54.211 1.570 Wilson plot Bfac: 18.00 37256 reflections ( 99.94 % complete ) and 0 restraints for refining 2005 atoms. Observations/parameters ratio is 4.65 ------------------------------------------------------ Starting model: R = 0.3261 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2718 (Rfree = 0.000) for 2005 atoms. Found 111 (136 requested) and removed 68 (68 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.78 1.71 NCS extension: 0 residues added, 2048 seeds are put forward Round 1: 182 peptides, 12 chains. Longest chain 38 peptides. Score 0.824 Round 2: 199 peptides, 5 chains. Longest chain 87 peptides. Score 0.917 Round 3: 203 peptides, 4 chains. Longest chain 91 peptides. Score 0.928 Round 4: 204 peptides, 5 chains. Longest chain 91 peptides. Score 0.922 Round 5: 203 peptides, 5 chains. Longest chain 85 peptides. Score 0.921 Taking the results from Round 3 Chains 4, Residues 199, Estimated correctness of the model 99.7 % 4 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 68 A Built loop between residues 19 B and 23 B 2 chains (205 residues) following loop building 2 chains (205 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1811 restraints for refining 1851 atoms. 242 conditional restraints added. Observations/parameters ratio is 5.03 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2733 (Rfree = 0.000) for 1851 atoms. Found 96 (126 requested) and removed 29 (63 requested) atoms. Cycle 2: After refmac, R = 0.2421 (Rfree = 0.000) for 1916 atoms. Found 86 (130 requested) and removed 16 (65 requested) atoms. Cycle 3: After refmac, R = 0.2275 (Rfree = 0.000) for 1982 atoms. Found 67 (135 requested) and removed 15 (67 requested) atoms. Cycle 4: After refmac, R = 0.2188 (Rfree = 0.000) for 2030 atoms. Found 58 (138 requested) and removed 25 (69 requested) atoms. Cycle 5: After refmac, R = 0.2144 (Rfree = 0.000) for 2056 atoms. Found 54 (140 requested) and removed 20 (70 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.74 1.67 NCS extension: 9 residues added (4 deleted due to clashes), 2102 seeds are put forward Round 1: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 2: 205 peptides, 4 chains. Longest chain 91 peptides. Score 0.930 Round 3: 207 peptides, 3 chains. Longest chain 104 peptides. Score 0.939 Round 4: 206 peptides, 4 chains. Longest chain 91 peptides. Score 0.931 Round 5: 205 peptides, 5 chains. Longest chain 104 peptides. Score 0.923 Taking the results from Round 3 Chains 3, Residues 204, Estimated correctness of the model 99.8 % 3 chains (204 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 20 B and 23 B 2 chains (206 residues) following loop building 2 chains (206 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1826 restraints for refining 1913 atoms. 248 conditional restraints added. Observations/parameters ratio is 4.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2343 (Rfree = 0.000) for 1913 atoms. Found 82 (130 requested) and removed 16 (65 requested) atoms. Cycle 7: After refmac, R = 0.2172 (Rfree = 0.000) for 1976 atoms. Found 54 (135 requested) and removed 13 (67 requested) atoms. Cycle 8: After refmac, R = 0.2086 (Rfree = 0.000) for 2012 atoms. Found 51 (137 requested) and removed 16 (68 requested) atoms. Cycle 9: After refmac, R = 0.2061 (Rfree = 0.000) for 2042 atoms. Found 58 (139 requested) and removed 29 (69 requested) atoms. Cycle 10: After refmac, R = 0.2035 (Rfree = 0.000) for 2070 atoms. Found 52 (141 requested) and removed 35 (70 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.74 1.67 NCS extension: 10 residues added (3 deleted due to clashes), 2100 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 3: 202 peptides, 4 chains. Longest chain 103 peptides. Score 0.927 Round 4: 204 peptides, 4 chains. Longest chain 91 peptides. Score 0.929 Round 5: 204 peptides, 4 chains. Longest chain 103 peptides. Score 0.929 Taking the results from Round 2 Chains 3, Residues 201, Estimated correctness of the model 99.8 % 2 chains (191 residues) have been docked in sequence Building loops using Loopy2018 3 chains (201 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1973 restraints for refining 1921 atoms. 470 conditional restraints added. Observations/parameters ratio is 4.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2117 (Rfree = 0.000) for 1921 atoms. Found 87 (128 requested) and removed 11 (65 requested) atoms. Cycle 12: After refmac, R = 0.2083 (Rfree = 0.000) for 1992 atoms. Found 61 (133 requested) and removed 25 (68 requested) atoms. Cycle 13: After refmac, R = 0.2040 (Rfree = 0.000) for 2025 atoms. Found 54 (135 requested) and removed 23 (69 requested) atoms. Cycle 14: After refmac, R = 0.2016 (Rfree = 0.000) for 2051 atoms. Found 56 (137 requested) and removed 27 (70 requested) atoms. Cycle 15: After refmac, R = 0.2002 (Rfree = 0.000) for 2074 atoms. Found 48 (138 requested) and removed 19 (70 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.73 1.66 NCS extension: 11 residues added (3 deleted due to clashes), 2115 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 3: 203 peptides, 4 chains. Longest chain 90 peptides. Score 0.928 Round 4: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 5: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Taking the results from Round 5 Chains 3, Residues 201, Estimated correctness of the model 99.8 % 3 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 B and 24 B 2 chains (205 residues) following loop building 2 chains (205 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1835 restraints for refining 1948 atoms. 266 conditional restraints added. Observations/parameters ratio is 4.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2120 (Rfree = 0.000) for 1948 atoms. Found 111 (130 requested) and removed 27 (66 requested) atoms. Cycle 17: After refmac, R = 0.2074 (Rfree = 0.000) for 2027 atoms. Found 63 (135 requested) and removed 27 (69 requested) atoms. Cycle 18: After refmac, R = 0.2022 (Rfree = 0.000) for 2058 atoms. Found 72 (137 requested) and removed 14 (70 requested) atoms. Cycle 19: After refmac, R = 0.2002 (Rfree = 0.000) for 2113 atoms. Found 59 (141 requested) and removed 31 (72 requested) atoms. Cycle 20: After refmac, R = 0.1974 (Rfree = 0.000) for 2131 atoms. Found 75 (140 requested) and removed 20 (73 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.74 1.67 NCS extension: 10 residues added (3 deleted due to clashes), 2197 seeds are put forward Round 1: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 2: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 3: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 4: 203 peptides, 5 chains. Longest chain 90 peptides. Score 0.921 Round 5: 204 peptides, 4 chains. Longest chain 103 peptides. Score 0.929 Taking the results from Round 3 Chains 3, Residues 202, Estimated correctness of the model 99.8 % 2 chains (191 residues) have been docked in sequence Building loops using Loopy2018 3 chains (202 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 2007 restraints for refining 1988 atoms. 500 conditional restraints added. Observations/parameters ratio is 4.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2125 (Rfree = 0.000) for 1988 atoms. Found 88 (130 requested) and removed 20 (67 requested) atoms. Cycle 22: After refmac, R = 0.2067 (Rfree = 0.000) for 2052 atoms. Found 67 (134 requested) and removed 20 (70 requested) atoms. Cycle 23: After refmac, R = 0.2033 (Rfree = 0.000) for 2095 atoms. Found 61 (137 requested) and removed 27 (71 requested) atoms. Cycle 24: After refmac, R = 0.1992 (Rfree = 0.000) for 2126 atoms. Found 61 (139 requested) and removed 28 (72 requested) atoms. Cycle 25: After refmac, R = 0.1987 (Rfree = 0.000) for 2153 atoms. Found 66 (141 requested) and removed 33 (73 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.74 1.67 NCS extension: 10 residues added (4 deleted due to clashes), 2197 seeds are put forward Round 1: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 2: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 3: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 4: 204 peptides, 4 chains. Longest chain 90 peptides. Score 0.929 Round 5: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Taking the results from Round 3 Chains 3, Residues 202, Estimated correctness of the model 99.8 % 2 chains (191 residues) have been docked in sequence Building loops using Loopy2018 3 chains (202 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 2001 restraints for refining 1982 atoms. 494 conditional restraints added. Observations/parameters ratio is 4.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2087 (Rfree = 0.000) for 1982 atoms. Found 111 (130 requested) and removed 16 (67 requested) atoms. Cycle 27: After refmac, R = 0.2070 (Rfree = 0.000) for 2073 atoms. Found 64 (135 requested) and removed 35 (70 requested) atoms. Cycle 28: After refmac, R = 0.2012 (Rfree = 0.000) for 2099 atoms. Found 59 (134 requested) and removed 26 (71 requested) atoms. Cycle 29: After refmac, R = 0.2002 (Rfree = 0.000) for 2126 atoms. Found 55 (136 requested) and removed 30 (72 requested) atoms. Cycle 30: After refmac, R = 0.1995 (Rfree = 0.000) for 2148 atoms. Found 57 (134 requested) and removed 27 (73 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.74 1.67 NCS extension: 11 residues added (3 deleted due to clashes), 2190 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 3: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 4: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 5: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Taking the results from Round 5 Chains 3, Residues 201, Estimated correctness of the model 99.8 % 3 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 24 A 2 chains (205 residues) following loop building 2 chains (205 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1909 restraints for refining 1996 atoms. 340 conditional restraints added. Observations/parameters ratio is 4.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2116 (Rfree = 0.000) for 1996 atoms. Found 113 (125 requested) and removed 23 (68 requested) atoms. Cycle 32: After refmac, R = 0.2066 (Rfree = 0.000) for 2085 atoms. Found 63 (131 requested) and removed 32 (71 requested) atoms. Cycle 33: After refmac, R = 0.1997 (Rfree = 0.000) for 2113 atoms. Found 53 (130 requested) and removed 21 (72 requested) atoms. Cycle 34: After refmac, R = 0.1973 (Rfree = 0.000) for 2136 atoms. Found 54 (131 requested) and removed 18 (73 requested) atoms. Cycle 35: After refmac, R = 0.1943 (Rfree = 0.000) for 2169 atoms. Found 58 (133 requested) and removed 25 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.73 1.66 NCS extension: 10 residues added (3 deleted due to clashes), 2213 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 3: 203 peptides, 4 chains. Longest chain 90 peptides. Score 0.928 Round 4: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 5: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Taking the results from Round 5 Chains 3, Residues 201, Estimated correctness of the model 99.8 % 2 chains (191 residues) have been docked in sequence Building loops using Loopy2018 3 chains (201 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 2038 restraints for refining 1985 atoms. 535 conditional restraints added. Observations/parameters ratio is 4.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2074 (Rfree = 0.000) for 1985 atoms. Found 116 (121 requested) and removed 21 (67 requested) atoms. Cycle 37: After refmac, R = 0.2051 (Rfree = 0.000) for 2075 atoms. Found 55 (127 requested) and removed 37 (70 requested) atoms. Cycle 38: After refmac, R = 0.2005 (Rfree = 0.000) for 2091 atoms. Found 70 (125 requested) and removed 21 (71 requested) atoms. Cycle 39: After refmac, R = 0.1993 (Rfree = 0.000) for 2133 atoms. Found 58 (128 requested) and removed 28 (73 requested) atoms. Cycle 40: After refmac, R = 0.1976 (Rfree = 0.000) for 2158 atoms. Found 66 (129 requested) and removed 34 (73 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.73 1.66 NCS extension: 11 residues added (3 deleted due to clashes), 2201 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 3: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 4: 203 peptides, 4 chains. Longest chain 90 peptides. Score 0.928 Round 5: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Taking the results from Round 5 Chains 3, Residues 201, Estimated correctness of the model 99.8 % 3 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 B and 24 B 2 chains (205 residues) following loop building 2 chains (205 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1881 restraints for refining 1981 atoms. 312 conditional restraints added. Observations/parameters ratio is 4.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2090 (Rfree = 0.000) for 1981 atoms. Found 95 (116 requested) and removed 24 (67 requested) atoms. Cycle 42: After refmac, R = 0.2049 (Rfree = 0.000) for 2047 atoms. Found 68 (120 requested) and removed 26 (69 requested) atoms. Cycle 43: After refmac, R = 0.1997 (Rfree = 0.000) for 2086 atoms. Found 55 (122 requested) and removed 27 (71 requested) atoms. Cycle 44: After refmac, R = 0.1976 (Rfree = 0.000) for 2105 atoms. Found 62 (124 requested) and removed 22 (72 requested) atoms. Cycle 45: After refmac, R = 0.1959 (Rfree = 0.000) for 2141 atoms. Found 48 (126 requested) and removed 36 (73 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.74 1.67 NCS extension: 10 residues added (3 deleted due to clashes), 2164 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 3: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 4: 202 peptides, 5 chains. Longest chain 85 peptides. Score 0.920 Round 5: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 201, Estimated correctness of the model 99.8 % 2 chains (191 residues) have been docked in sequence Sequence coverage is 94 % All DUM atoms will be removed Building loops using Loopy2018 3 chains (201 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 37256 reflections ( 99.94 % complete ) and 1503 restraints for refining 1475 atoms. Observations/parameters ratio is 6.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2605 (Rfree = 0.000) for 1475 atoms. Found 54 (84 requested) and removed 0 (84 requested) atoms. Cycle 47: After refmac, R = 0.2433 (Rfree = 0.000) for 1475 atoms. Found 31 (87 requested) and removed 0 (52 requested) atoms. Cycle 48: After refmac, R = 0.2301 (Rfree = 0.000) for 1475 atoms. Found 13 (89 requested) and removed 2 (53 requested) atoms. Cycle 49: After refmac, R = 0.2240 (Rfree = 0.000) for 1475 atoms. Found 9 (90 requested) and removed 4 (53 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:14:51 GMT 2018 Job finished. TimeTaking 51.86 Used memory is bytes: 19300888