Mon 24 Dec 00:20:58 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 2o1q-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.2-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/2o1q-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.2-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 00:21:03 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/2o1q-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.2-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 186 and 0 Target number of residues in the AU: 186 Target solvent content: 0.6061 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-3.2-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.65 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 3 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: 56.142 3.200 Wilson plot Bfac: 54.88 4668 reflections ( 99.79 % complete ) and 0 restraints for refining 2587 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3204 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3029 (Rfree = 0.000) for 2587 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 2620 seeds are put forward NCS extension: 0 residues added, 2620 seeds are put forward Round 1: 145 peptides, 26 chains. Longest chain 13 peptides. Score 0.435 Round 2: 181 peptides, 25 chains. Longest chain 22 peptides. Score 0.636 Round 3: 188 peptides, 22 chains. Longest chain 27 peptides. Score 0.713 Round 4: 186 peptides, 21 chains. Longest chain 17 peptides. Score 0.721 Round 5: 194 peptides, 20 chains. Longest chain 28 peptides. Score 0.760 Taking the results from Round 5 Chains 20, Residues 174, Estimated correctness of the model 76.9 % 5 chains (58 residues) have been docked in sequence Building loops using Loopy2018 20 chains (174 residues) following loop building 5 chains (58 residues) in sequence following loop building ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 3942 restraints for refining 2114 atoms. 3037 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2958 (Rfree = 0.000) for 2114 atoms. Found 16 (19 requested) and removed 17 (9 requested) atoms. Cycle 2: After refmac, R = 0.2565 (Rfree = 0.000) for 2068 atoms. Found 14 (18 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2625 (Rfree = 0.000) for 2053 atoms. Found 11 (17 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2635 (Rfree = 0.000) for 2036 atoms. Found 13 (17 requested) and removed 12 (9 requested) atoms. Cycle 5: After refmac, R = 0.2289 (Rfree = 0.000) for 2025 atoms. Found 11 (17 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 2079 seeds are put forward NCS extension: 31 residues added (7 deleted due to clashes), 2110 seeds are put forward Round 1: 155 peptides, 21 chains. Longest chain 17 peptides. Score 0.599 Round 2: 189 peptides, 24 chains. Longest chain 23 peptides. Score 0.684 Round 3: 189 peptides, 18 chains. Longest chain 22 peptides. Score 0.773 Round 4: 182 peptides, 22 chains. Longest chain 19 peptides. Score 0.692 Round 5: 182 peptides, 22 chains. Longest chain 17 peptides. Score 0.692 Taking the results from Round 3 Chains 23, Residues 171, Estimated correctness of the model 79.1 % 7 chains (87 residues) have been docked in sequence Building loops using Loopy2018 23 chains (171 residues) following loop building 7 chains (87 residues) in sequence following loop building ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 3736 restraints for refining 2117 atoms. 2760 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2837 (Rfree = 0.000) for 2117 atoms. Found 17 (17 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.2551 (Rfree = 0.000) for 2097 atoms. Found 16 (16 requested) and removed 15 (9 requested) atoms. Cycle 8: After refmac, R = 0.2423 (Rfree = 0.000) for 2081 atoms. Found 15 (15 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2430 (Rfree = 0.000) for 2079 atoms. Found 15 (15 requested) and removed 13 (9 requested) atoms. Cycle 10: After refmac, R = 0.2087 (Rfree = 0.000) for 2075 atoms. Found 8 (15 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.59 Search for helices and strands: 0 residues in 0 chains, 2110 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 2126 seeds are put forward Round 1: 161 peptides, 23 chains. Longest chain 19 peptides. Score 0.586 Round 2: 182 peptides, 21 chains. Longest chain 19 peptides. Score 0.708 Round 3: 182 peptides, 23 chains. Longest chain 19 peptides. Score 0.675 Round 4: 173 peptides, 19 chains. Longest chain 22 peptides. Score 0.708 Round 5: 180 peptides, 19 chains. Longest chain 28 peptides. Score 0.732 Taking the results from Round 5 Chains 20, Residues 161, Estimated correctness of the model 71.7 % 3 chains (43 residues) have been docked in sequence Building loops using Loopy2018 20 chains (161 residues) following loop building 3 chains (43 residues) in sequence following loop building ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4288 restraints for refining 2118 atoms. 3490 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3042 (Rfree = 0.000) for 2118 atoms. Found 15 (15 requested) and removed 18 (9 requested) atoms. Cycle 12: After refmac, R = 0.2669 (Rfree = 0.000) for 2104 atoms. Found 14 (14 requested) and removed 16 (9 requested) atoms. Cycle 13: After refmac, R = 0.2152 (Rfree = 0.000) for 2084 atoms. Found 11 (14 requested) and removed 12 (9 requested) atoms. Cycle 14: After refmac, R = 0.2389 (Rfree = 0.000) for 2081 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2285 (Rfree = 0.000) for 2078 atoms. Found 12 (13 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.59 Search for helices and strands: 0 residues in 0 chains, 2120 seeds are put forward NCS extension: 32 residues added (4 deleted due to clashes), 2152 seeds are put forward Round 1: 158 peptides, 21 chains. Longest chain 18 peptides. Score 0.613 Round 2: 168 peptides, 22 chains. Longest chain 18 peptides. Score 0.637 Round 3: 168 peptides, 18 chains. Longest chain 20 peptides. Score 0.707 Round 4: 171 peptides, 20 chains. Longest chain 21 peptides. Score 0.685 Round 5: 160 peptides, 20 chains. Longest chain 19 peptides. Score 0.641 Taking the results from Round 3 Chains 19, Residues 150, Estimated correctness of the model 66.7 % 5 chains (54 residues) have been docked in sequence Building loops using Loopy2018 19 chains (150 residues) following loop building 5 chains (54 residues) in sequence following loop building ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4217 restraints for refining 2118 atoms. 3414 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2695 (Rfree = 0.000) for 2118 atoms. Found 13 (13 requested) and removed 14 (9 requested) atoms. Cycle 17: After refmac, R = 0.2726 (Rfree = 0.000) for 2112 atoms. Found 12 (12 requested) and removed 11 (9 requested) atoms. Cycle 18: After refmac, R = 0.2724 (Rfree = 0.000) for 2107 atoms. Found 12 (12 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.2609 (Rfree = 0.000) for 2099 atoms. Found 12 (12 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2639 (Rfree = 0.000) for 2095 atoms. Found 11 (11 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.59 Search for helices and strands: 0 residues in 0 chains, 2141 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2157 seeds are put forward Round 1: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.448 Round 2: 170 peptides, 24 chains. Longest chain 20 peptides. Score 0.607 Round 3: 179 peptides, 24 chains. Longest chain 20 peptides. Score 0.646 Round 4: 172 peptides, 25 chains. Longest chain 17 peptides. Score 0.597 Round 5: 169 peptides, 23 chains. Longest chain 19 peptides. Score 0.622 Taking the results from Round 3 Chains 26, Residues 155, Estimated correctness of the model 52.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4460 restraints for refining 2111 atoms. 3799 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2938 (Rfree = 0.000) for 2111 atoms. Found 11 (11 requested) and removed 15 (9 requested) atoms. Cycle 22: After refmac, R = 0.2343 (Rfree = 0.000) for 2100 atoms. Found 11 (11 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.2178 (Rfree = 0.000) for 2091 atoms. Found 11 (11 requested) and removed 12 (9 requested) atoms. Cycle 24: After refmac, R = 0.2463 (Rfree = 0.000) for 2088 atoms. Found 11 (11 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2617 (Rfree = 0.000) for 2087 atoms. Found 11 (11 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 2129 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 2150 seeds are put forward Round 1: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.481 Round 2: 149 peptides, 19 chains. Longest chain 17 peptides. Score 0.613 Round 3: 146 peptides, 20 chains. Longest chain 16 peptides. Score 0.578 Round 4: 159 peptides, 19 chains. Longest chain 21 peptides. Score 0.656 Round 5: 157 peptides, 22 chains. Longest chain 21 peptides. Score 0.588 Taking the results from Round 4 Chains 20, Residues 140, Estimated correctness of the model 55.3 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4549 restraints for refining 2118 atoms. 3942 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3095 (Rfree = 0.000) for 2118 atoms. Found 11 (11 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.2449 (Rfree = 0.000) for 2099 atoms. Found 11 (11 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.2265 (Rfree = 0.000) for 2087 atoms. Found 7 (11 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.2077 (Rfree = 0.000) for 2074 atoms. Found 11 (11 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.2656 (Rfree = 0.000) for 2071 atoms. Found 11 (11 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 2099 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2117 seeds are put forward Round 1: 146 peptides, 22 chains. Longest chain 26 peptides. Score 0.534 Round 2: 160 peptides, 19 chains. Longest chain 20 peptides. Score 0.660 Round 3: 163 peptides, 18 chains. Longest chain 29 peptides. Score 0.689 Round 4: 161 peptides, 18 chains. Longest chain 33 peptides. Score 0.681 Round 5: 157 peptides, 15 chains. Longest chain 29 peptides. Score 0.718 Taking the results from Round 5 Chains 15, Residues 142, Estimated correctness of the model 68.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4505 restraints for refining 2095 atoms. 3952 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2969 (Rfree = 0.000) for 2095 atoms. Found 11 (11 requested) and removed 20 (9 requested) atoms. Cycle 32: After refmac, R = 0.2968 (Rfree = 0.000) for 2078 atoms. Found 10 (10 requested) and removed 14 (9 requested) atoms. Cycle 33: After refmac, R = 0.2918 (Rfree = 0.000) for 2068 atoms. Found 10 (10 requested) and removed 12 (9 requested) atoms. Cycle 34: After refmac, R = 0.2276 (Rfree = 0.000) for 2062 atoms. Found 10 (10 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2033 (Rfree = 0.000) for 2061 atoms. Found 9 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 2101 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 2122 seeds are put forward Round 1: 120 peptides, 21 chains. Longest chain 13 peptides. Score 0.412 Round 2: 136 peptides, 21 chains. Longest chain 19 peptides. Score 0.504 Round 3: 135 peptides, 20 chains. Longest chain 15 peptides. Score 0.522 Round 4: 141 peptides, 20 chains. Longest chain 13 peptides. Score 0.553 Round 5: 142 peptides, 20 chains. Longest chain 15 peptides. Score 0.558 Taking the results from Round 5 Chains 20, Residues 122, Estimated correctness of the model 29.2 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4311 restraints for refining 2050 atoms. 3771 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2822 (Rfree = 0.000) for 2050 atoms. Found 9 (9 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.2715 (Rfree = 0.000) for 2030 atoms. Found 9 (9 requested) and removed 16 (9 requested) atoms. Cycle 38: After refmac, R = 0.2185 (Rfree = 0.000) for 2022 atoms. Found 8 (9 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.2363 (Rfree = 0.000) for 2017 atoms. Found 9 (9 requested) and removed 13 (9 requested) atoms. Cycle 40: After refmac, R = 0.2101 (Rfree = 0.000) for 2011 atoms. Found 7 (9 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 2046 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2060 seeds are put forward Round 1: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.438 Round 2: 118 peptides, 18 chains. Longest chain 19 peptides. Score 0.477 Round 3: 129 peptides, 19 chains. Longest chain 13 peptides. Score 0.514 Round 4: 119 peptides, 16 chains. Longest chain 15 peptides. Score 0.532 Round 5: 121 peptides, 15 chains. Longest chain 16 peptides. Score 0.565 Taking the results from Round 5 Chains 15, Residues 106, Estimated correctness of the model 31.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4471 restraints for refining 2029 atoms. 4062 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2660 (Rfree = 0.000) for 2029 atoms. Found 9 (9 requested) and removed 15 (9 requested) atoms. Cycle 42: After refmac, R = 0.2671 (Rfree = 0.000) for 2017 atoms. Found 9 (9 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2076 (Rfree = 0.000) for 2007 atoms. Found 4 (9 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.2420 (Rfree = 0.000) for 1997 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.2057 (Rfree = 0.000) for 1994 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2050 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.361 Round 2: 125 peptides, 21 chains. Longest chain 11 peptides. Score 0.442 Round 3: 129 peptides, 18 chains. Longest chain 16 peptides. Score 0.537 Round 4: 130 peptides, 18 chains. Longest chain 16 peptides. Score 0.542 Round 5: 133 peptides, 19 chains. Longest chain 13 peptides. Score 0.535 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 112, Estimated correctness of the model 24.5 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4668 reflections ( 99.79 % complete ) and 4163 restraints for refining 1954 atoms. 3726 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2677 (Rfree = 0.000) for 1954 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2548 (Rfree = 0.000) for 1943 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1989 (Rfree = 0.000) for 1934 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2243 (Rfree = 0.000) for 1924 atoms. TimeTaking 33.95