Mon 24 Dec 07:40:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oh1-1.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-1.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-1.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-noncs ############### 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 07:40:40 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/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 5728 target number of atoms Had to go as low as 0.40 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 6370 atoms. Observations/parameters ratio is 5.00 ------------------------------------------------------ Starting model: R = 0.3178 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2603 (Rfree = 0.000) for 6370 atoms. Found 513 (535 requested) and removed 251 (267 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.67 1.63 Round 1: 626 peptides, 26 chains. Longest chain 99 peptides. Score 0.895 Round 2: 657 peptides, 15 chains. Longest chain 125 peptides. Score 0.932 Round 3: 664 peptides, 12 chains. Longest chain 171 peptides. Score 0.940 Round 4: 665 peptides, 13 chains. Longest chain 141 peptides. Score 0.938 Round 5: 664 peptides, 11 chains. Longest chain 134 peptides. Score 0.942 Taking the results from Round 5 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 6511 restraints for refining 6361 atoms. 1150 conditional restraints added. Observations/parameters ratio is 5.00 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2698 (Rfree = 0.000) for 6361 atoms. Found 322 (534 requested) and removed 95 (267 requested) atoms. Cycle 2: After refmac, R = 0.2376 (Rfree = 0.000) for 6583 atoms. Found 251 (553 requested) and removed 34 (276 requested) atoms. Cycle 3: After refmac, R = 0.2242 (Rfree = 0.000) for 6784 atoms. Found 185 (571 requested) and removed 37 (285 requested) atoms. Cycle 4: After refmac, R = 0.2153 (Rfree = 0.000) for 6915 atoms. Found 203 (582 requested) and removed 42 (291 requested) atoms. Cycle 5: After refmac, R = 0.2097 (Rfree = 0.000) for 7057 atoms. Found 181 (594 requested) and removed 36 (297 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.63 1.59 Round 1: 670 peptides, 10 chains. Longest chain 170 peptides. Score 0.946 Round 2: 672 peptides, 10 chains. Longest chain 171 peptides. Score 0.946 Round 3: 674 peptides, 10 chains. Longest chain 171 peptides. Score 0.946 Round 4: 670 peptides, 13 chains. Longest chain 133 peptides. Score 0.940 Round 5: 672 peptides, 12 chains. Longest chain 171 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 6672 restraints for refining 6764 atoms. 1206 conditional restraints added. Observations/parameters ratio is 4.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2221 (Rfree = 0.000) for 6764 atoms. Found 300 (568 requested) and removed 64 (284 requested) atoms. Cycle 7: After refmac, R = 0.2151 (Rfree = 0.000) for 6983 atoms. Found 182 (588 requested) and removed 48 (294 requested) atoms. Cycle 8: After refmac, R = 0.2074 (Rfree = 0.000) for 7104 atoms. Found 171 (597 requested) and removed 58 (298 requested) atoms. Cycle 9: After refmac, R = 0.2023 (Rfree = 0.000) for 7200 atoms. Found 203 (606 requested) and removed 43 (303 requested) atoms. Cycle 10: After refmac, R = 0.1998 (Rfree = 0.000) for 7342 atoms. Found 175 (618 requested) and removed 59 (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: 678 peptides, 8 chains. Longest chain 171 peptides. Score 0.951 Round 3: 673 peptides, 12 chains. Longest chain 151 peptides. Score 0.942 Round 4: 673 peptides, 12 chains. Longest chain 134 peptides. Score 0.942 Round 5: 679 peptides, 9 chains. Longest chain 171 peptides. Score 0.950 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 6768 restraints for refining 6966 atoms. 1255 conditional restraints added. Observations/parameters ratio is 4.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2171 (Rfree = 0.000) for 6966 atoms. Found 330 (585 requested) and removed 78 (292 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2113 (Rfree = 0.000) for 7199 atoms. Found 226 (606 requested) and removed 63 (303 requested) atoms. Cycle 13: After refmac, R = 0.2075 (Rfree = 0.000) for 7344 atoms. Found 181 (618 requested) and removed 94 (309 requested) atoms. Cycle 14: After refmac, R = 0.2021 (Rfree = 0.000) for 7415 atoms. Found 200 (612 requested) and removed 59 (312 requested) atoms. Cycle 15: After refmac, R = 0.2012 (Rfree = 0.000) for 7531 atoms. Found 214 (621 requested) and removed 88 (317 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.63 1.59 Round 1: 671 peptides, 10 chains. Longest chain 171 peptides. Score 0.946 Round 2: 675 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 3: 670 peptides, 13 chains. Longest chain 151 peptides. Score 0.940 Round 4: 674 peptides, 9 chains. Longest chain 171 peptides. Score 0.948 Round 5: 679 peptides, 8 chains. Longest chain 171 peptides. Score 0.951 Taking the results from Round 5 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 6875 restraints for refining 7078 atoms. 1328 conditional restraints added. Observations/parameters ratio is 4.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2222 (Rfree = 0.000) for 7078 atoms. Found 359 (582 requested) and removed 121 (297 requested) atoms. Cycle 17: After refmac, R = 0.2161 (Rfree = 0.000) for 7299 atoms. Found 208 (602 requested) and removed 61 (307 requested) atoms. Cycle 18: After refmac, R = 0.2086 (Rfree = 0.000) for 7426 atoms. Found 182 (612 requested) and removed 51 (312 requested) atoms. Cycle 19: After refmac, R = 0.2038 (Rfree = 0.000) for 7541 atoms. Found 165 (621 requested) and removed 54 (317 requested) atoms. Cycle 20: After refmac, R = 0.1997 (Rfree = 0.000) for 7633 atoms. Found 172 (629 requested) and removed 77 (321 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.63 1.59 Round 1: 678 peptides, 8 chains. Longest chain 171 peptides. Score 0.951 Round 2: 682 peptides, 6 chains. Longest chain 171 peptides. Score 0.956 Round 3: 677 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 4: 675 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 5: 674 peptides, 11 chains. Longest chain 171 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 6955 restraints for refining 7167 atoms. 1361 conditional restraints added. Observations/parameters ratio is 4.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2187 (Rfree = 0.000) for 7167 atoms. Found 349 (590 requested) and removed 86 (301 requested) atoms. Cycle 22: After refmac, R = 0.2140 (Rfree = 0.000) for 7413 atoms. Found 203 (612 requested) and removed 60 (312 requested) atoms. Cycle 23: After refmac, R = 0.2076 (Rfree = 0.000) for 7531 atoms. Found 161 (621 requested) and removed 51 (317 requested) atoms. Cycle 24: After refmac, R = 0.2030 (Rfree = 0.000) for 7621 atoms. Found 161 (628 requested) and removed 57 (320 requested) atoms. Cycle 25: After refmac, R = 0.1993 (Rfree = 0.000) for 7706 atoms. Found 158 (635 requested) and removed 46 (324 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.63 1.59 Round 1: 678 peptides, 8 chains. Longest chain 171 peptides. Score 0.951 Round 2: 678 peptides, 8 chains. Longest chain 171 peptides. Score 0.951 Round 3: 672 peptides, 10 chains. Longest chain 171 peptides. Score 0.946 Round 4: 675 peptides, 11 chains. Longest chain 135 peptides. Score 0.945 Round 5: 673 peptides, 12 chains. Longest chain 171 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 7170 restraints for refining 7239 atoms. 1628 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2162 (Rfree = 0.000) for 7239 atoms. Found 332 (596 requested) and removed 81 (304 requested) atoms. Cycle 27: After refmac, R = 0.2111 (Rfree = 0.000) for 7470 atoms. Found 184 (616 requested) and removed 42 (314 requested) atoms. Cycle 28: After refmac, R = 0.2051 (Rfree = 0.000) for 7589 atoms. Found 185 (626 requested) and removed 53 (319 requested) atoms. Cycle 29: After refmac, R = 0.1999 (Rfree = 0.000) for 7699 atoms. Found 152 (635 requested) and removed 55 (324 requested) atoms. Cycle 30: After refmac, R = 0.1974 (Rfree = 0.000) for 7764 atoms. Found 172 (641 requested) and removed 74 (327 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.63 1.59 Round 1: 675 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 2: 678 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 3: 671 peptides, 11 chains. Longest chain 171 peptides. Score 0.944 Round 4: 676 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 5: 677 peptides, 11 chains. Longest chain 171 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 7204 restraints for refining 7244 atoms. 1668 conditional restraints added. Observations/parameters ratio is 4.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2166 (Rfree = 0.000) for 7244 atoms. Found 343 (596 requested) and removed 102 (304 requested) atoms. Cycle 32: After refmac, R = 0.2098 (Rfree = 0.000) for 7474 atoms. Found 189 (615 requested) and removed 52 (314 requested) atoms. Cycle 33: After refmac, R = 0.2020 (Rfree = 0.000) for 7595 atoms. Found 178 (626 requested) and removed 43 (319 requested) atoms. Cycle 34: After refmac, R = 0.1982 (Rfree = 0.000) for 7711 atoms. Found 154 (636 requested) and removed 74 (324 requested) atoms. Cycle 35: After refmac, R = 0.1945 (Rfree = 0.000) for 7768 atoms. Found 180 (641 requested) and removed 75 (327 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.63 1.59 Round 1: 676 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 2: 680 peptides, 7 chains. Longest chain 171 peptides. Score 0.953 Round 3: 678 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 4: 675 peptides, 11 chains. Longest chain 171 peptides. Score 0.945 Round 5: 672 peptides, 11 chains. Longest chain 133 peptides. Score 0.944 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 7072 restraints for refining 7260 atoms. 1503 conditional restraints added. Observations/parameters ratio is 4.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2140 (Rfree = 0.000) for 7260 atoms. Found 384 (597 requested) and removed 87 (304 requested) atoms. Cycle 37: After refmac, R = 0.2104 (Rfree = 0.000) for 7533 atoms. Found 213 (621 requested) and removed 62 (317 requested) atoms. Cycle 38: After refmac, R = 0.2035 (Rfree = 0.000) for 7662 atoms. Found 192 (632 requested) and removed 53 (322 requested) atoms. Cycle 39: After refmac, R = 0.1987 (Rfree = 0.000) for 7786 atoms. Found 186 (642 requested) and removed 81 (327 requested) atoms. Cycle 40: After refmac, R = 0.1961 (Rfree = 0.000) for 7872 atoms. Found 190 (649 requested) and removed 97 (331 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.63 1.59 Round 1: 678 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 2: 681 peptides, 6 chains. Longest chain 171 peptides. Score 0.955 Round 3: 678 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 4: 676 peptides, 11 chains. Longest chain 170 peptides. Score 0.945 Round 5: 678 peptides, 10 chains. Longest chain 171 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 7142 restraints for refining 7297 atoms. 1554 conditional restraints added. Observations/parameters ratio is 4.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2156 (Rfree = 0.000) for 7297 atoms. Found 386 (588 requested) and removed 99 (306 requested) atoms. Cycle 42: After refmac, R = 0.2115 (Rfree = 0.000) for 7565 atoms. Found 237 (612 requested) and removed 67 (318 requested) atoms. Cycle 43: After refmac, R = 0.2062 (Rfree = 0.000) for 7712 atoms. Found 197 (623 requested) and removed 88 (324 requested) atoms. Cycle 44: After refmac, R = 0.2010 (Rfree = 0.000) for 7808 atoms. Found 190 (630 requested) and removed 79 (328 requested) atoms. Cycle 45: After refmac, R = 0.1982 (Rfree = 0.000) for 7889 atoms. Found 206 (638 requested) and removed 81 (332 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.63 1.59 Round 1: 674 peptides, 10 chains. Longest chain 165 peptides. Score 0.946 Round 2: 681 peptides, 5 chains. Longest chain 171 peptides. Score 0.957 Round 3: 671 peptides, 12 chains. Longest chain 171 peptides. Score 0.942 Round 4: 680 peptides, 7 chains. Longest chain 171 peptides. Score 0.953 Round 5: 670 peptides, 15 chains. Longest chain 171 peptides. Score 0.936 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 7171 restraints for refining 7326 atoms. 1574 conditional restraints added. Observations/parameters ratio is 4.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2168 (Rfree = 0.000) for 7326 atoms. Found 0 (590 requested) and removed 10 (307 requested) atoms. Cycle 47: After refmac, R = 0.2062 (Rfree = 0.000) for 7293 atoms. Found 0 (577 requested) and removed 2 (307 requested) atoms. Cycle 48: After refmac, R = 0.1999 (Rfree = 0.000) for 7280 atoms. Found 0 (563 requested) and removed 0 (306 requested) atoms. Cycle 49: After refmac, R = 0.1957 (Rfree = 0.000) for 7271 atoms. TimeTaking 76.72