Tue 25 Dec 19:27:57 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 2o2x-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-1.5-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/2o2x-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-1.5-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 ============================================================ Tue 25 Dec 19:28:07 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/2o2x-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-1.5-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 203 and 0 Target number of residues in the AU: 203 Target solvent content: 0.4153 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 218 Adjusted target solvent content: 0.37 Input MTZ file: 2o2x-1.5-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: 4 Cell parameters: 36.470 66.250 41.010 90.000 108.540 90.000 Input sequence file: 2o2x-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 1744 target number of atoms Had to go as low as 0.25 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: 38.882 1.500 Wilson plot Bfac: 9.56 28753 reflections ( 97.06 % complete ) and 0 restraints for refining 1932 atoms. Observations/parameters ratio is 3.72 ------------------------------------------------------ Starting model: R = 0.3155 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2672 (Rfree = 0.000) for 1932 atoms. Found 137 (150 requested) and removed 77 (75 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.40 1.67 Round 1: 192 peptides, 10 chains. Longest chain 54 peptides. Score 0.925 Round 2: 198 peptides, 5 chains. Longest chain 79 peptides. Score 0.961 Round 3: 200 peptides, 3 chains. Longest chain 96 peptides. Score 0.972 Round 4: 202 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 5: 202 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Taking the results from Round 5 Chains 3, Residues 200, Estimated correctness of the model 100.0 % 2 chains (197 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 134 A and 140 A 1 chains (202 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ 28753 reflections ( 97.06 % complete ) and 1762 restraints for refining 1815 atoms. 209 conditional restraints added. Observations/parameters ratio is 3.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2598 (Rfree = 0.000) for 1815 atoms. Found 58 (141 requested) and removed 20 (70 requested) atoms. Cycle 2: After refmac, R = 0.2323 (Rfree = 0.000) for 1851 atoms. Found 64 (144 requested) and removed 6 (72 requested) atoms. Cycle 3: After refmac, R = 0.1994 (Rfree = 0.000) for 1905 atoms. Found 73 (148 requested) and removed 16 (74 requested) atoms. Cycle 4: After refmac, R = 0.1885 (Rfree = 0.000) for 1955 atoms. Found 59 (152 requested) and removed 17 (76 requested) atoms. Cycle 5: After refmac, R = 0.1804 (Rfree = 0.000) for 1991 atoms. Found 58 (155 requested) and removed 18 (77 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.38 1.65 Round 1: 200 peptides, 3 chains. Longest chain 121 peptides. Score 0.972 Round 2: 202 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 3: 203 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 4: 203 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 5: 203 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Taking the results from Round 5 Chains 3, Residues 201, Estimated correctness of the model 100.0 % 2 chains (198 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 134 A and 139 A 1 chains (202 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ 28753 reflections ( 97.06 % complete ) and 1806 restraints for refining 1910 atoms. 253 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2185 (Rfree = 0.000) for 1910 atoms. Found 65 (148 requested) and removed 23 (74 requested) atoms. Cycle 7: After refmac, R = 0.1879 (Rfree = 0.000) for 1949 atoms. Found 71 (151 requested) and removed 6 (75 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1798 (Rfree = 0.000) for 2007 atoms. Found 67 (156 requested) and removed 8 (78 requested) atoms. Cycle 9: After refmac, R = 0.1739 (Rfree = 0.000) for 2060 atoms. Found 53 (160 requested) and removed 17 (80 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1692 (Rfree = 0.000) for 2092 atoms. Found 53 (163 requested) and removed 15 (81 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.38 1.65 Round 1: 201 peptides, 4 chains. Longest chain 122 peptides. Score 0.968 Round 2: 202 peptides, 3 chains. Longest chain 129 peptides. Score 0.973 Round 3: 200 peptides, 2 chains. Longest chain 129 peptides. Score 0.977 Round 4: 203 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 5: 201 peptides, 3 chains. Longest chain 122 peptides. Score 0.973 Taking the results from Round 4 Chains 3, Residues 201, Estimated correctness of the model 100.0 % 2 chains (197 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 133 A and 139 A 1 chains (202 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ 28753 reflections ( 97.06 % complete ) and 1879 restraints for refining 1972 atoms. 323 conditional restraints added. Observations/parameters ratio is 3.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 1972 atoms. Found 75 (153 requested) and removed 24 (76 requested) atoms. Cycle 12: After refmac, R = 0.1854 (Rfree = 0.000) for 2021 atoms. Found 62 (157 requested) and removed 12 (78 requested) atoms. Cycle 13: After refmac, R = 0.1783 (Rfree = 0.000) for 2059 atoms. Found 57 (161 requested) and removed 18 (80 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1734 (Rfree = 0.000) for 2096 atoms. Found 51 (163 requested) and removed 22 (81 requested) atoms. Cycle 15: After refmac, R = 0.1693 (Rfree = 0.000) for 2115 atoms. Found 49 (165 requested) and removed 26 (82 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.36 1.62 Round 1: 198 peptides, 3 chains. Longest chain 122 peptides. Score 0.971 Round 2: 203 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 3: 202 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 4: 201 peptides, 3 chains. Longest chain 128 peptides. Score 0.973 Round 5: 198 peptides, 3 chains. Longest chain 129 peptides. Score 0.971 Taking the results from Round 3 Chains 2, Residues 200, Estimated correctness of the model 100.0 % 2 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 139 A 1 chains (202 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 28753 reflections ( 97.06 % complete ) and 1865 restraints for refining 1978 atoms. 309 conditional restraints added. Observations/parameters ratio is 3.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2144 (Rfree = 0.000) for 1978 atoms. Found 76 (150 requested) and removed 24 (76 requested) atoms. Cycle 17: After refmac, R = 0.1851 (Rfree = 0.000) for 2026 atoms. Found 61 (154 requested) and removed 13 (78 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1762 (Rfree = 0.000) for 2064 atoms. Found 63 (158 requested) and removed 8 (80 requested) atoms. Cycle 19: After refmac, R = 0.1731 (Rfree = 0.000) for 2113 atoms. Found 46 (161 requested) and removed 24 (82 requested) atoms. Cycle 20: After refmac, R = 0.1678 (Rfree = 0.000) for 2121 atoms. Found 58 (159 requested) and removed 20 (83 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.37 1.64 Round 1: 200 peptides, 3 chains. Longest chain 122 peptides. Score 0.972 Round 2: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 3: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 4: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 5: 201 peptides, 3 chains. Longest chain 122 peptides. Score 0.973 Taking the results from Round 4 Chains 2, Residues 200, Estimated correctness of the model 100.0 % 2 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 1 chains (202 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ 28753 reflections ( 97.06 % complete ) and 1850 restraints for refining 1992 atoms. 294 conditional restraints added. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2144 (Rfree = 0.000) for 1992 atoms. Found 77 (148 requested) and removed 27 (77 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1850 (Rfree = 0.000) for 2037 atoms. Found 71 (152 requested) and removed 16 (79 requested) atoms. Cycle 23: After refmac, R = 0.1774 (Rfree = 0.000) for 2084 atoms. Found 68 (156 requested) and removed 15 (81 requested) atoms. Cycle 24: After refmac, R = 0.1715 (Rfree = 0.000) for 2132 atoms. Found 54 (159 requested) and removed 27 (83 requested) atoms. Cycle 25: After refmac, R = 0.1681 (Rfree = 0.000) for 2154 atoms. Found 58 (160 requested) and removed 30 (83 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.37 1.64 Round 1: 200 peptides, 3 chains. Longest chain 122 peptides. Score 0.972 Round 2: 200 peptides, 2 chains. Longest chain 129 peptides. Score 0.977 Round 3: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 4: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 5: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Taking the results from Round 5 Chains 2, Residues 200, Estimated correctness of the model 100.0 % 2 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 1 chains (202 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 28753 reflections ( 97.06 % complete ) and 1897 restraints for refining 2000 atoms. 341 conditional restraints added. Observations/parameters ratio is 3.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2147 (Rfree = 0.000) for 2000 atoms. Found 86 (146 requested) and removed 21 (77 requested) atoms. Cycle 27: After refmac, R = 0.1892 (Rfree = 0.000) for 2059 atoms. Found 65 (150 requested) and removed 11 (80 requested) atoms. Cycle 28: After refmac, R = 0.1806 (Rfree = 0.000) for 2106 atoms. Found 53 (154 requested) and removed 20 (82 requested) atoms. Cycle 29: After refmac, R = 0.1723 (Rfree = 0.000) for 2132 atoms. Found 67 (156 requested) and removed 17 (83 requested) atoms. Cycle 30: After refmac, R = 0.1698 (Rfree = 0.000) for 2175 atoms. Found 62 (159 requested) and removed 26 (84 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.37 1.64 Round 1: 201 peptides, 3 chains. Longest chain 122 peptides. Score 0.973 Round 2: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 3: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 4: 199 peptides, 2 chains. Longest chain 129 peptides. Score 0.977 Round 5: 202 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Taking the results from Round 5 Chains 2, Residues 200, Estimated correctness of the model 100.0 % 2 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 1 chains (202 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ 28753 reflections ( 97.06 % complete ) and 1927 restraints for refining 2027 atoms. 371 conditional restraints added. Observations/parameters ratio is 3.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2101 (Rfree = 0.000) for 2027 atoms. Found 102 (148 requested) and removed 25 (78 requested) atoms. Cycle 32: After refmac, R = 0.1851 (Rfree = 0.000) for 2098 atoms. Found 73 (153 requested) and removed 14 (81 requested) atoms. Cycle 33: After refmac, R = 0.1772 (Rfree = 0.000) for 2152 atoms. Found 59 (157 requested) and removed 20 (83 requested) atoms. Cycle 34: After refmac, R = 0.1720 (Rfree = 0.000) for 2186 atoms. Found 57 (160 requested) and removed 18 (85 requested) atoms. Cycle 35: After refmac, R = 0.1709 (Rfree = 0.000) for 2215 atoms. Found 72 (163 requested) and removed 37 (86 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.37 1.64 Round 1: 200 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 2: 200 peptides, 3 chains. Longest chain 113 peptides. Score 0.972 Round 3: 202 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 4: 202 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 5: 199 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Taking the results from Round 4 Chains 3, Residues 200, Estimated correctness of the model 100.0 % 2 chains (197 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 134 A and 139 A 1 chains (201 residues) following loop building 1 chains (201 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 28753 reflections ( 97.06 % complete ) and 1988 restraints for refining 2050 atoms. 443 conditional restraints added. Observations/parameters ratio is 3.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2157 (Rfree = 0.000) for 2050 atoms. Found 93 (146 requested) and removed 24 (79 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1879 (Rfree = 0.000) for 2116 atoms. Found 55 (151 requested) and removed 7 (82 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1789 (Rfree = 0.000) for 2154 atoms. Found 60 (155 requested) and removed 7 (84 requested) atoms. Cycle 39: After refmac, R = 0.1737 (Rfree = 0.000) for 2200 atoms. Found 49 (157 requested) and removed 18 (85 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1698 (Rfree = 0.000) for 2220 atoms. Found 61 (159 requested) and removed 21 (86 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.37 1.64 Round 1: 198 peptides, 3 chains. Longest chain 113 peptides. Score 0.971 Round 2: 200 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 3: 198 peptides, 3 chains. Longest chain 113 peptides. Score 0.971 Round 4: 200 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 5: 200 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Taking the results from Round 5 Chains 3, Residues 198, Estimated correctness of the model 100.0 % 2 chains (195 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 134 A and 140 A 1 chains (200 residues) following loop building 1 chains (200 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 28753 reflections ( 97.06 % complete ) and 2052 restraints for refining 2060 atoms. 514 conditional restraints added. Observations/parameters ratio is 3.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2168 (Rfree = 0.000) for 2060 atoms. Found 82 (147 requested) and removed 26 (80 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1866 (Rfree = 0.000) for 2112 atoms. Found 76 (151 requested) and removed 11 (82 requested) atoms. Cycle 43: After refmac, R = 0.1778 (Rfree = 0.000) for 2169 atoms. Found 55 (155 requested) and removed 13 (84 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1728 (Rfree = 0.000) for 2200 atoms. Found 56 (157 requested) and removed 24 (85 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1688 (Rfree = 0.000) for 2223 atoms. Found 64 (159 requested) and removed 29 (86 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.37 1.64 Round 1: 199 peptides, 3 chains. Longest chain 112 peptides. Score 0.972 Round 2: 201 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 3: 199 peptides, 3 chains. Longest chain 112 peptides. Score 0.972 Round 4: 198 peptides, 2 chains. Longest chain 127 peptides. Score 0.976 Round 5: 199 peptides, 3 chains. Longest chain 112 peptides. Score 0.972 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 199, Estimated correctness of the model 100.0 % 2 chains (196 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 134 A and 140 A 1 chains (201 residues) following loop building 1 chains (201 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 28753 reflections ( 97.06 % complete ) and 1545 restraints for refining 1511 atoms. Observations/parameters ratio is 4.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2747 (Rfree = 0.000) for 1511 atoms. Found 78 (108 requested) and removed 0 (108 requested) atoms. Cycle 47: After refmac, R = 0.2315 (Rfree = 0.000) for 1511 atoms. Found 50 (113 requested) and removed 0 (61 requested) atoms. Cycle 48: After refmac, R = 0.2095 (Rfree = 0.000) for 1511 atoms. Found 38 (117 requested) and removed 0 (63 requested) atoms. Cycle 49: After refmac, R = 0.1943 (Rfree = 0.000) for 1511 atoms. Found 13 (120 requested) and removed 1 (65 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:15:52 GMT 2018 Job finished. TimeTaking 47.91