Mon 24 Dec 00:42:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ooc-1.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-1.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-1.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:42:59 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-1.6-parrot-mrncs/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-mrncs.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-mrncs.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 2008 atoms. Observations/parameters ratio is 4.64 ------------------------------------------------------ Starting model: R = 0.3304 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2717 (Rfree = 0.000) for 2008 atoms. Found 100 (137 requested) and removed 71 (68 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.78 1.71 NCS extension: 0 residues added, 2037 seeds are put forward Round 1: 176 peptides, 12 chains. Longest chain 39 peptides. Score 0.810 Round 2: 191 peptides, 6 chains. Longest chain 82 peptides. Score 0.899 Round 3: 198 peptides, 5 chains. Longest chain 53 peptides. Score 0.916 Round 4: 200 peptides, 3 chains. Longest chain 103 peptides. Score 0.932 Round 5: 199 peptides, 4 chains. Longest chain 85 peptides. Score 0.924 Taking the results from Round 4 Chains 3, Residues 197, Estimated correctness of the model 99.8 % 3 chains (197 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 20 A and 24 A 2 chains (200 residues) following loop building 2 chains (200 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1859 restraints for refining 1856 atoms. 332 conditional restraints added. Observations/parameters ratio is 5.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2700 (Rfree = 0.000) for 1856 atoms. Found 91 (126 requested) and removed 28 (63 requested) atoms. Cycle 2: After refmac, R = 0.2348 (Rfree = 0.000) for 1919 atoms. Found 71 (130 requested) and removed 25 (65 requested) atoms. Cycle 3: After refmac, R = 0.2209 (Rfree = 0.000) for 1959 atoms. Found 62 (134 requested) and removed 19 (67 requested) atoms. Cycle 4: After refmac, R = 0.2136 (Rfree = 0.000) for 1992 atoms. Found 67 (136 requested) and removed 15 (68 requested) atoms. Cycle 5: After refmac, R = 0.2081 (Rfree = 0.000) for 2039 atoms. Found 48 (139 requested) and removed 24 (69 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.74 1.67 NCS extension: 11 residues added (5 deleted due to clashes), 2077 seeds are put forward Round 1: 205 peptides, 4 chains. Longest chain 103 peptides. Score 0.930 Round 2: 205 peptides, 4 chains. Longest chain 103 peptides. Score 0.930 Round 3: 204 peptides, 5 chains. Longest chain 86 peptides. Score 0.922 Round 4: 201 peptides, 3 chains. Longest chain 103 peptides. Score 0.933 Round 5: 206 peptides, 3 chains. Longest chain 103 peptides. Score 0.938 Taking the results from Round 5 Chains 3, Residues 203, Estimated correctness of the model 99.8 % 2 chains (196 residues) have been docked in sequence Building loops using Loopy2018 3 chains (203 residues) following loop building 2 chains (196 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1887 restraints for refining 1907 atoms. 362 conditional restraints added. Observations/parameters ratio is 4.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2181 (Rfree = 0.000) for 1907 atoms. Found 107 (130 requested) and removed 24 (65 requested) atoms. Cycle 7: After refmac, R = 0.2132 (Rfree = 0.000) for 1989 atoms. Found 57 (135 requested) and removed 22 (67 requested) atoms. Cycle 8: After refmac, R = 0.2068 (Rfree = 0.000) for 2020 atoms. Found 57 (138 requested) and removed 14 (69 requested) atoms. Cycle 9: After refmac, R = 0.2052 (Rfree = 0.000) for 2053 atoms. Found 62 (140 requested) and removed 18 (70 requested) atoms. Cycle 10: After refmac, R = 0.2032 (Rfree = 0.000) for 2093 atoms. Found 76 (143 requested) and removed 21 (71 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.74 1.67 NCS extension: 9 residues added (3 deleted due to clashes), 2159 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: 204 peptides, 4 chains. Longest chain 90 peptides. Score 0.929 Round 4: 204 peptides, 4 chains. Longest chain 103 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 202, Estimated correctness of the model 99.8 % 3 chains (202 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 20 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 1866 restraints for refining 1958 atoms. 297 conditional restraints added. Observations/parameters ratio is 4.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2130 (Rfree = 0.000) for 1958 atoms. Found 98 (133 requested) and removed 20 (66 requested) atoms. Cycle 12: After refmac, R = 0.2072 (Rfree = 0.000) for 2030 atoms. Found 56 (138 requested) and removed 23 (69 requested) atoms. Cycle 13: After refmac, R = 0.2027 (Rfree = 0.000) for 2062 atoms. Found 50 (140 requested) and removed 19 (70 requested) atoms. Cycle 14: After refmac, R = 0.1999 (Rfree = 0.000) for 2089 atoms. Found 49 (142 requested) and removed 25 (71 requested) atoms. Cycle 15: After refmac, R = 0.1982 (Rfree = 0.000) for 2108 atoms. Found 56 (141 requested) and removed 20 (72 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.74 1.67 NCS extension: 9 residues added (4 deleted due to clashes), 2156 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: 203 peptides, 5 chains. Longest chain 74 peptides. Score 0.921 Round 4: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 5: 204 peptides, 4 chains. Longest chain 90 peptides. Score 0.929 Taking the results from Round 4 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 1965 restraints for refining 1950 atoms. 458 conditional restraints added. Observations/parameters ratio is 4.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2104 (Rfree = 0.000) for 1950 atoms. Found 109 (130 requested) and removed 18 (66 requested) atoms. Cycle 17: After refmac, R = 0.2089 (Rfree = 0.000) for 2036 atoms. Found 58 (136 requested) and removed 27 (69 requested) atoms. Cycle 18: After refmac, R = 0.2029 (Rfree = 0.000) for 2067 atoms. Found 60 (138 requested) and removed 18 (70 requested) atoms. Cycle 19: After refmac, R = 0.2005 (Rfree = 0.000) for 2104 atoms. Found 53 (140 requested) and removed 18 (71 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1978 (Rfree = 0.000) for 2130 atoms. Found 54 (142 requested) and removed 20 (72 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.74 1.67 NCS extension: 11 residues added (3 deleted due to clashes), 2177 seeds are put forward Round 1: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 2: 204 peptides, 4 chains. Longest chain 103 peptides. Score 0.929 Round 3: 205 peptides, 3 chains. Longest chain 103 peptides. Score 0.937 Round 4: 202 peptides, 6 chains. Longest chain 90 peptides. Score 0.913 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 % 3 chains (202 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 20 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 1847 restraints for refining 1976 atoms. 278 conditional restraints added. Observations/parameters ratio is 4.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2093 (Rfree = 0.000) for 1976 atoms. Found 112 (131 requested) and removed 11 (67 requested) atoms. Cycle 22: After refmac, R = 0.2082 (Rfree = 0.000) for 2072 atoms. Found 73 (138 requested) and removed 26 (70 requested) atoms. Cycle 23: After refmac, R = 0.2049 (Rfree = 0.000) for 2115 atoms. Found 49 (141 requested) and removed 33 (72 requested) atoms. Cycle 24: After refmac, R = 0.1996 (Rfree = 0.000) for 2126 atoms. Found 56 (139 requested) and removed 27 (72 requested) atoms. Cycle 25: After refmac, R = 0.1981 (Rfree = 0.000) for 2148 atoms. Found 48 (140 requested) and removed 29 (73 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.74 1.67 NCS extension: 9 residues added (4 deleted due to clashes), 2178 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 204 peptides, 4 chains. Longest chain 103 peptides. Score 0.929 Round 3: 203 peptides, 5 chains. Longest chain 91 peptides. Score 0.921 Round 4: 203 peptides, 5 chains. Longest chain 103 peptides. Score 0.921 Round 5: 204 peptides, 4 chains. Longest chain 91 peptides. Score 0.929 Taking the results from Round 1 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 1996 restraints for refining 1989 atoms. 493 conditional restraints added. Observations/parameters ratio is 4.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2081 (Rfree = 0.000) for 1989 atoms. Found 99 (127 requested) and removed 11 (67 requested) atoms. Cycle 27: After refmac, R = 0.2045 (Rfree = 0.000) for 2072 atoms. Found 59 (133 requested) and removed 21 (70 requested) atoms. Cycle 28: After refmac, R = 0.1995 (Rfree = 0.000) for 2103 atoms. Found 58 (134 requested) and removed 17 (71 requested) atoms. Cycle 29: After refmac, R = 0.1976 (Rfree = 0.000) for 2135 atoms. Found 55 (137 requested) and removed 14 (73 requested) atoms. Cycle 30: After refmac, R = 0.1945 (Rfree = 0.000) for 2165 atoms. Found 52 (139 requested) and removed 26 (74 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.74 1.67 NCS extension: 11 residues added (3 deleted due to clashes), 2202 seeds are put forward Round 1: 203 peptides, 4 chains. Longest chain 103 peptides. Score 0.928 Round 2: 203 peptides, 4 chains. Longest chain 90 peptides. Score 0.928 Round 3: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 4: 202 peptides, 5 chains. Longest chain 90 peptides. Score 0.920 Round 5: 203 peptides, 4 chains. Longest chain 103 peptides. Score 0.928 Taking the results from Round 3 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 1884 restraints for refining 1997 atoms. 315 conditional restraints added. Observations/parameters ratio is 4.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2101 (Rfree = 0.000) for 1997 atoms. Found 107 (128 requested) and removed 16 (68 requested) atoms. Cycle 32: After refmac, R = 0.2055 (Rfree = 0.000) for 2083 atoms. Found 60 (133 requested) and removed 20 (71 requested) atoms. Cycle 33: After refmac, R = 0.2000 (Rfree = 0.000) for 2114 atoms. Found 63 (135 requested) and removed 22 (72 requested) atoms. Cycle 34: After refmac, R = 0.1984 (Rfree = 0.000) for 2146 atoms. Found 60 (137 requested) and removed 25 (73 requested) atoms. Cycle 35: After refmac, R = 0.1985 (Rfree = 0.000) for 2172 atoms. Found 59 (139 requested) and removed 26 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.74 1.67 NCS extension: 0 residues added, 2205 seeds are put forward Round 1: 203 peptides, 3 chains. Longest chain 103 peptides. Score 0.935 Round 2: 202 peptides, 5 chains. Longest chain 56 peptides. Score 0.920 Round 3: 202 peptides, 4 chains. Longest chain 89 peptides. Score 0.927 Round 4: 202 peptides, 4 chains. Longest chain 103 peptides. Score 0.927 Round 5: 202 peptides, 4 chains. Longest chain 89 peptides. Score 0.927 Taking the results from Round 1 Chains 3, Residues 200, Estimated correctness of the model 99.8 % 3 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 B and 24 B 2 chains (204 residues) following loop building 2 chains (204 residues) in sequence following loop building ------------------------------------------------------ 37256 reflections ( 99.94 % complete ) and 1893 restraints for refining 1992 atoms. 333 conditional restraints added. Observations/parameters ratio is 4.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2113 (Rfree = 0.000) for 1992 atoms. Found 105 (128 requested) and removed 23 (68 requested) atoms. Cycle 37: After refmac, R = 0.2086 (Rfree = 0.000) for 2069 atoms. Found 67 (133 requested) and removed 22 (70 requested) atoms. Cycle 38: After refmac, R = 0.2026 (Rfree = 0.000) for 2110 atoms. Found 54 (135 requested) and removed 18 (72 requested) atoms. Cycle 39: After refmac, R = 0.1991 (Rfree = 0.000) for 2139 atoms. Found 55 (137 requested) and removed 16 (73 requested) atoms. Cycle 40: After refmac, R = 0.1961 (Rfree = 0.000) for 2171 atoms. Found 53 (139 requested) and removed 32 (74 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.74 1.67 NCS extension: 0 residues added, 2192 seeds are put forward Round 1: 203 peptides, 3 chains. Longest chain 103 peptides. Score 0.935 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: 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 1904 restraints for refining 2000 atoms. 335 conditional restraints added. Observations/parameters ratio is 4.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2090 (Rfree = 0.000) for 2000 atoms. Found 101 (125 requested) and removed 19 (68 requested) atoms. Cycle 42: After refmac, R = 0.2057 (Rfree = 0.000) for 2072 atoms. Found 73 (131 requested) and removed 31 (71 requested) atoms. Cycle 43: After refmac, R = 0.2034 (Rfree = 0.000) for 2110 atoms. Found 69 (132 requested) and removed 27 (72 requested) atoms. Cycle 44: After refmac, R = 0.2017 (Rfree = 0.000) for 2146 atoms. Found 65 (134 requested) and removed 32 (73 requested) atoms. Cycle 45: After refmac, R = 0.2004 (Rfree = 0.000) for 2172 atoms. Found 61 (136 requested) and removed 32 (74 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.74 1.67 NCS extension: 9 residues added (3 deleted due to clashes), 2211 seeds are put forward Round 1: 204 peptides, 3 chains. Longest chain 103 peptides. Score 0.936 Round 2: 203 peptides, 4 chains. Longest chain 90 peptides. Score 0.928 Round 3: 203 peptides, 4 chains. Longest chain 103 peptides. Score 0.928 Round 4: 203 peptides, 4 chains. Longest chain 90 peptides. Score 0.928 Round 5: 201 peptides, 6 chains. Longest chain 74 peptides. Score 0.911 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 201, Estimated correctness of the model 99.8 % 3 chains (201 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed 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 ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 37256 reflections ( 99.94 % complete ) and 1569 restraints for refining 1537 atoms. Observations/parameters ratio is 6.06 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2536 (Rfree = 0.000) for 1537 atoms. Found 51 (94 requested) and removed 0 (94 requested) atoms. Cycle 47: After refmac, R = 0.2355 (Rfree = 0.000) for 1537 atoms. Found 32 (97 requested) and removed 0 (54 requested) atoms. Cycle 48: After refmac, R = 0.2224 (Rfree = 0.000) for 1537 atoms. Found 18 (99 requested) and removed 1 (55 requested) atoms. Cycle 49: After refmac, R = 0.2140 (Rfree = 0.000) for 1537 atoms. Found 10 (100 requested) and removed 1 (55 requested) atoms. Writing output files ... TimeTaking 42.12