Mon 24 Dec 00:03:54 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 2oh1-1.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-1.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-1.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-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/2oh1-1.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-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 00:04:00 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/2oh1-1.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-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 803 and 0 Target number of residues in the AU: 803 Target solvent content: 0.4606 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-1.5-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: 19 Cell parameters: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-1.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5728 target number of atoms Had to go as low as 0.50 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: 77.501 1.460 Wilson plot Bfac: 16.22 127339 reflections ( 90.67 % complete ) and 0 restraints for refining 6347 atoms. Observations/parameters ratio is 5.02 ------------------------------------------------------ Starting model: R = 0.3250 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2654 (Rfree = 0.000) for 6347 atoms. Found 511 (533 requested) and removed 266 (266 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.67 1.63 Round 1: 646 peptides, 22 chains. Longest chain 96 peptides. Score 0.913 Round 2: 662 peptides, 14 chains. Longest chain 137 peptides. Score 0.935 Round 3: 672 peptides, 10 chains. Longest chain 146 peptides. Score 0.946 Round 4: 664 peptides, 12 chains. Longest chain 152 peptides. Score 0.940 Round 5: 666 peptides, 10 chains. Longest chain 171 peptides. Score 0.945 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6352 restraints for refining 6348 atoms. 873 conditional restraints added. Observations/parameters ratio is 5.01 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2739 (Rfree = 0.000) for 6348 atoms. Found 265 (533 requested) and removed 98 (266 requested) atoms. Cycle 2: After refmac, R = 0.2562 (Rfree = 0.000) for 6514 atoms. Found 198 (547 requested) and removed 31 (273 requested) atoms. Cycle 3: After refmac, R = 0.2324 (Rfree = 0.000) for 6671 atoms. Found 180 (561 requested) and removed 29 (280 requested) atoms. Cycle 4: After refmac, R = 0.2217 (Rfree = 0.000) for 6799 atoms. Found 194 (573 requested) and removed 29 (286 requested) atoms. Cycle 5: After refmac, R = 0.2129 (Rfree = 0.000) for 6952 atoms. Found 173 (584 requested) and removed 33 (292 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 1.60 Round 1: 671 peptides, 11 chains. Longest chain 138 peptides. Score 0.944 Round 2: 677 peptides, 8 chains. Longest chain 172 peptides. Score 0.951 Round 3: 675 peptides, 11 chains. Longest chain 152 peptides. Score 0.945 Round 4: 679 peptides, 9 chains. Longest chain 172 peptides. Score 0.950 Round 5: 676 peptides, 10 chains. Longest chain 145 peptides. Score 0.947 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6562 restraints for refining 6774 atoms. 1020 conditional restraints added. Observations/parameters ratio is 4.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2262 (Rfree = 0.000) for 6774 atoms. Found 300 (569 requested) and removed 72 (284 requested) atoms. Cycle 7: After refmac, R = 0.2179 (Rfree = 0.000) for 6989 atoms. Found 197 (588 requested) and removed 38 (294 requested) atoms. Cycle 8: After refmac, R = 0.2104 (Rfree = 0.000) for 7138 atoms. Found 184 (600 requested) and removed 43 (300 requested) atoms. Cycle 9: After refmac, R = 0.2062 (Rfree = 0.000) for 7258 atoms. Found 165 (611 requested) and removed 61 (305 requested) atoms. Cycle 10: After refmac, R = 0.2009 (Rfree = 0.000) for 7352 atoms. Found 183 (618 requested) and removed 54 (309 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.63 1.59 Round 1: 672 peptides, 9 chains. Longest chain 171 peptides. Score 0.948 Round 2: 679 peptides, 6 chains. Longest chain 172 peptides. Score 0.955 Round 3: 678 peptides, 8 chains. Longest chain 172 peptides. Score 0.951 Round 4: 680 peptides, 6 chains. Longest chain 172 peptides. Score 0.955 Round 5: 677 peptides, 10 chains. Longest chain 134 peptides. Score 0.947 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6652 restraints for refining 6960 atoms. 1065 conditional restraints added. Observations/parameters ratio is 4.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2200 (Rfree = 0.000) for 6960 atoms. Found 358 (584 requested) and removed 73 (292 requested) atoms. Cycle 12: After refmac, R = 0.2144 (Rfree = 0.000) for 7234 atoms. Found 189 (608 requested) and removed 51 (304 requested) atoms. Cycle 13: After refmac, R = 0.2072 (Rfree = 0.000) for 7356 atoms. Found 176 (619 requested) and removed 44 (309 requested) atoms. Cycle 14: After refmac, R = 0.2023 (Rfree = 0.000) for 7473 atoms. Found 179 (629 requested) and removed 48 (314 requested) atoms. Cycle 15: After refmac, R = 0.1998 (Rfree = 0.000) for 7579 atoms. Found 197 (638 requested) and removed 56 (319 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.63 1.59 Round 1: 674 peptides, 8 chains. Longest chain 172 peptides. Score 0.950 Round 2: 677 peptides, 6 chains. Longest chain 172 peptides. Score 0.955 Round 3: 671 peptides, 12 chains. Longest chain 152 peptides. Score 0.942 Round 4: 671 peptides, 9 chains. Longest chain 171 peptides. Score 0.948 Round 5: 668 peptides, 10 chains. Longest chain 172 peptides. Score 0.945 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6894 restraints for refining 7130 atoms. 1327 conditional restraints added. Observations/parameters ratio is 4.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2193 (Rfree = 0.000) for 7130 atoms. Found 340 (599 requested) and removed 89 (299 requested) atoms. Cycle 17: After refmac, R = 0.2155 (Rfree = 0.000) for 7363 atoms. Found 183 (620 requested) and removed 41 (310 requested) atoms. Cycle 18: After refmac, R = 0.2078 (Rfree = 0.000) for 7493 atoms. Found 172 (630 requested) and removed 53 (315 requested) atoms. Cycle 19: After refmac, R = 0.2037 (Rfree = 0.000) for 7593 atoms. Found 168 (639 requested) and removed 63 (319 requested) atoms. Cycle 20: After refmac, R = 0.2010 (Rfree = 0.000) for 7672 atoms. Found 176 (646 requested) and removed 67 (323 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.63 1.59 Round 1: 671 peptides, 10 chains. Longest chain 166 peptides. Score 0.946 Round 2: 677 peptides, 6 chains. Longest chain 172 peptides. Score 0.955 Round 3: 674 peptides, 11 chains. Longest chain 172 peptides. Score 0.945 Round 4: 676 peptides, 7 chains. Longest chain 172 peptides. Score 0.953 Round 5: 673 peptides, 12 chains. Longest chain 134 peptides. Score 0.942 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6986 restraints for refining 7183 atoms. 1421 conditional restraints added. Observations/parameters ratio is 4.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2184 (Rfree = 0.000) for 7183 atoms. Found 348 (603 requested) and removed 85 (301 requested) atoms. Cycle 22: After refmac, R = 0.2146 (Rfree = 0.000) for 7432 atoms. Found 195 (625 requested) and removed 49 (312 requested) atoms. Cycle 23: After refmac, R = 0.2066 (Rfree = 0.000) for 7563 atoms. Found 194 (636 requested) and removed 50 (318 requested) atoms. Cycle 24: After refmac, R = 0.2028 (Rfree = 0.000) for 7684 atoms. Found 166 (647 requested) and removed 62 (323 requested) atoms. Cycle 25: After refmac, R = 0.2004 (Rfree = 0.000) for 7764 atoms. Found 168 (654 requested) and removed 64 (327 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.63 1.59 Round 1: 674 peptides, 11 chains. Longest chain 172 peptides. Score 0.945 Round 2: 674 peptides, 11 chains. Longest chain 172 peptides. Score 0.945 Round 3: 674 peptides, 10 chains. Longest chain 171 peptides. Score 0.946 Round 4: 675 peptides, 11 chains. Longest chain 162 peptides. Score 0.945 Round 5: 671 peptides, 12 chains. Longest chain 172 peptides. Score 0.942 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7235 restraints for refining 7265 atoms. 1748 conditional restraints added. Observations/parameters ratio is 4.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2190 (Rfree = 0.000) for 7265 atoms. Found 327 (610 requested) and removed 88 (305 requested) atoms. Cycle 27: After refmac, R = 0.2127 (Rfree = 0.000) for 7484 atoms. Found 177 (630 requested) and removed 40 (315 requested) atoms. Cycle 28: After refmac, R = 0.2066 (Rfree = 0.000) for 7599 atoms. Found 164 (640 requested) and removed 25 (320 requested) atoms. Cycle 29: After refmac, R = 0.2012 (Rfree = 0.000) for 7710 atoms. Found 188 (650 requested) and removed 50 (325 requested) atoms. Cycle 30: After refmac, R = 0.1974 (Rfree = 0.000) for 7821 atoms. Found 170 (659 requested) and removed 47 (329 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.63 1.59 Round 1: 677 peptides, 9 chains. Longest chain 172 peptides. Score 0.949 Round 2: 678 peptides, 9 chains. Longest chain 172 peptides. Score 0.949 Round 3: 677 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 4: 674 peptides, 9 chains. Longest chain 165 peptides. Score 0.948 Round 5: 678 peptides, 10 chains. Longest chain 172 peptides. Score 0.947 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7188 restraints for refining 7285 atoms. 1676 conditional restraints added. Observations/parameters ratio is 4.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2173 (Rfree = 0.000) for 7285 atoms. Found 370 (611 requested) and removed 87 (305 requested) atoms. Cycle 32: After refmac, R = 0.2127 (Rfree = 0.000) for 7550 atoms. Found 203 (635 requested) and removed 58 (317 requested) atoms. Cycle 33: After refmac, R = 0.2052 (Rfree = 0.000) for 7684 atoms. Found 176 (646 requested) and removed 47 (323 requested) atoms. Cycle 34: After refmac, R = 0.2003 (Rfree = 0.000) for 7792 atoms. Found 175 (656 requested) and removed 58 (328 requested) atoms. Cycle 35: After refmac, R = 0.1973 (Rfree = 0.000) for 7876 atoms. Found 174 (664 requested) and removed 76 (332 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.63 1.59 Round 1: 673 peptides, 11 chains. Longest chain 172 peptides. Score 0.944 Round 2: 674 peptides, 10 chains. Longest chain 172 peptides. Score 0.946 Round 3: 676 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 4: 674 peptides, 10 chains. Longest chain 171 peptides. Score 0.946 Round 5: 675 peptides, 12 chains. Longest chain 172 peptides. Score 0.943 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7239 restraints for refining 7335 atoms. 1727 conditional restraints added. Observations/parameters ratio is 4.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2188 (Rfree = 0.000) for 7335 atoms. Found 360 (616 requested) and removed 91 (308 requested) atoms. Cycle 37: After refmac, R = 0.2125 (Rfree = 0.000) for 7586 atoms. Found 224 (638 requested) and removed 41 (319 requested) atoms. Cycle 38: After refmac, R = 0.2055 (Rfree = 0.000) for 7750 atoms. Found 185 (652 requested) and removed 65 (326 requested) atoms. Cycle 39: After refmac, R = 0.2018 (Rfree = 0.000) for 7839 atoms. Found 178 (661 requested) and removed 71 (330 requested) atoms. Cycle 40: After refmac, R = 0.1975 (Rfree = 0.000) for 7922 atoms. Found 213 (667 requested) and removed 73 (333 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.63 1.59 Round 1: 670 peptides, 12 chains. Longest chain 166 peptides. Score 0.942 Round 2: 676 peptides, 8 chains. Longest chain 172 peptides. Score 0.951 Round 3: 669 peptides, 12 chains. Longest chain 152 peptides. Score 0.941 Round 4: 668 peptides, 14 chains. Longest chain 167 peptides. Score 0.937 Round 5: 669 peptides, 14 chains. Longest chain 134 peptides. Score 0.937 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 127339 reflections ( 90.67 % complete ) and 7166 restraints for refining 7341 atoms. 1634 conditional restraints added. Observations/parameters ratio is 4.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2179 (Rfree = 0.000) for 7341 atoms. Found 387 (616 requested) and removed 92 (308 requested) atoms. Cycle 42: After refmac, R = 0.2131 (Rfree = 0.000) for 7622 atoms. Found 211 (641 requested) and removed 58 (320 requested) atoms. Cycle 43: After refmac, R = 0.2068 (Rfree = 0.000) for 7750 atoms. Found 195 (653 requested) and removed 47 (326 requested) atoms. Cycle 44: After refmac, R = 0.2026 (Rfree = 0.000) for 7882 atoms. Found 181 (663 requested) and removed 69 (331 requested) atoms. Cycle 45: After refmac, R = 0.1999 (Rfree = 0.000) for 7965 atoms. Found 192 (671 requested) and removed 83 (335 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.63 1.59 Round 1: 670 peptides, 11 chains. Longest chain 171 peptides. Score 0.944 Round 2: 672 peptides, 10 chains. Longest chain 172 peptides. Score 0.946 Round 3: 669 peptides, 13 chains. Longest chain 152 peptides. Score 0.939 Round 4: 670 peptides, 12 chains. Longest chain 172 peptides. Score 0.942 Round 5: 668 peptides, 13 chains. Longest chain 134 peptides. Score 0.939 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2oh1-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 127339 reflections ( 90.67 % complete ) and 7415 restraints for refining 7369 atoms. 1958 conditional restraints added. Observations/parameters ratio is 4.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2183 (Rfree = 0.000) for 7369 atoms. Found 0 (619 requested) and removed 14 (309 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 7331 atoms. Found 0 (605 requested) and removed 1 (308 requested) atoms. Cycle 48: After refmac, R = 0.2017 (Rfree = 0.000) for 7319 atoms. Found 0 (590 requested) and removed 2 (307 requested) atoms. Cycle 49: After refmac, R = 0.1978 (Rfree = 0.000) for 7313 atoms. Found 0 (577 requested) and removed 0 (307 requested) atoms. Writing output files ... TimeTaking 96.6