null Mon 24 Dec 07:35:25 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 2o1q-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.2-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/2o1q-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.2-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 07:35:30 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/2o1q-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.2-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 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-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.2-parrot-noncs.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 2579 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2777 (Rfree = 0.000) for 2579 atoms. Found 14 (23 requested) and removed 42 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 3.49 Search for helices and strands: 0 residues in 0 chains, 2573 seeds are put forward NCS extension: 0 residues added, 2573 seeds are put forward Round 1: 142 peptides, 26 chains. Longest chain 14 peptides. Score 0.417 Round 2: 178 peptides, 29 chains. Longest chain 12 peptides. Score 0.544 Round 3: 185 peptides, 29 chains. Longest chain 13 peptides. Score 0.577 Round 4: 175 peptides, 25 chains. Longest chain 13 peptides. Score 0.610 Round 5: 172 peptides, 23 chains. Longest chain 19 peptides. Score 0.635 Taking the results from Round 5 Chains 25, Residues 149, Estimated correctness of the model 50.2 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4516 restraints for refining 2118 atoms. 3892 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2624 (Rfree = 0.000) for 2118 atoms. Found 16 (19 requested) and removed 16 (9 requested) atoms. Cycle 2: After refmac, R = 0.2707 (Rfree = 0.000) for 2098 atoms. Found 11 (19 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.2717 (Rfree = 0.000) for 2081 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 4: After refmac, R = 0.2556 (Rfree = 0.000) for 2079 atoms. Found 13 (18 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2486 (Rfree = 0.000) for 2071 atoms. Found 12 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2167 seeds are put forward Round 1: 144 peptides, 24 chains. Longest chain 18 peptides. Score 0.477 Round 2: 170 peptides, 25 chains. Longest chain 19 peptides. Score 0.588 Round 3: 172 peptides, 26 chains. Longest chain 14 peptides. Score 0.577 Round 4: 161 peptides, 23 chains. Longest chain 20 peptides. Score 0.586 Round 5: 160 peptides, 23 chains. Longest chain 22 peptides. Score 0.582 Taking the results from Round 2 Chains 26, Residues 145, Estimated correctness of the model 37.8 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4427 restraints for refining 2118 atoms. 3770 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2799 (Rfree = 0.000) for 2118 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 7: After refmac, R = 0.2848 (Rfree = 0.000) for 2107 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 8: After refmac, R = 0.2376 (Rfree = 0.000) for 2100 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 9: After refmac, R = 0.2810 (Rfree = 0.000) for 2101 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.2303 (Rfree = 0.000) for 2097 atoms. Found 15 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 2141 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2160 seeds are put forward Round 1: 164 peptides, 27 chains. Longest chain 16 peptides. Score 0.516 Round 2: 173 peptides, 26 chains. Longest chain 20 peptides. Score 0.581 Round 3: 167 peptides, 22 chains. Longest chain 19 peptides. Score 0.633 Round 4: 173 peptides, 21 chains. Longest chain 20 peptides. Score 0.675 Round 5: 165 peptides, 22 chains. Longest chain 20 peptides. Score 0.624 Taking the results from Round 4 Chains 24, Residues 152, Estimated correctness of the model 59.7 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4355 restraints for refining 2118 atoms. 3670 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3163 (Rfree = 0.000) for 2118 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 12: After refmac, R = 0.3225 (Rfree = 0.000) for 2102 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.2555 (Rfree = 0.000) for 2096 atoms. Found 17 (18 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.2395 (Rfree = 0.000) for 2094 atoms. Found 10 (18 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.2671 (Rfree = 0.000) for 2088 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 2129 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2146 seeds are put forward Round 1: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.459 Round 2: 152 peptides, 20 chains. Longest chain 19 peptides. Score 0.606 Round 3: 151 peptides, 19 chains. Longest chain 19 peptides. Score 0.622 Round 4: 155 peptides, 20 chains. Longest chain 18 peptides. Score 0.619 Round 5: 147 peptides, 19 chains. Longest chain 17 peptides. Score 0.604 Taking the results from Round 3 Chains 19, Residues 132, Estimated correctness of the model 46.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4791 restraints for refining 2118 atoms. 4282 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3097 (Rfree = 0.000) for 2118 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 17: After refmac, R = 0.3153 (Rfree = 0.000) for 2115 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 18: After refmac, R = 0.2816 (Rfree = 0.000) for 2107 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.2829 (Rfree = 0.000) for 2104 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2812 (Rfree = 0.000) for 2103 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 3.47 Search for helices and strands: 0 residues in 0 chains, 2173 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 2200 seeds are put forward Round 1: 119 peptides, 20 chains. Longest chain 12 peptides. Score 0.432 Round 2: 132 peptides, 18 chains. Longest chain 17 peptides. Score 0.553 Round 3: 137 peptides, 18 chains. Longest chain 17 peptides. Score 0.578 Round 4: 136 peptides, 20 chains. Longest chain 19 peptides. Score 0.528 Round 5: 136 peptides, 17 chains. Longest chain 18 peptides. Score 0.594 Taking the results from Round 5 Chains 17, Residues 119, Estimated correctness of the model 39.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4663 restraints for refining 2100 atoms. 4204 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2765 (Rfree = 0.000) for 2100 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 22: After refmac, R = 0.2782 (Rfree = 0.000) for 2093 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.2549 (Rfree = 0.000) for 2092 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.2085 (Rfree = 0.000) for 2097 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1958 (Rfree = 0.000) for 2094 atoms. Found 10 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2169 seeds are put forward Round 1: 113 peptides, 19 chains. Longest chain 16 peptides. Score 0.422 Round 2: 123 peptides, 19 chains. Longest chain 17 peptides. Score 0.481 Round 3: 125 peptides, 19 chains. Longest chain 18 peptides. Score 0.492 Round 4: 125 peptides, 17 chains. Longest chain 18 peptides. Score 0.540 Round 5: 122 peptides, 18 chains. Longest chain 13 peptides. Score 0.500 Taking the results from Round 4 Chains 17, Residues 108, Estimated correctness of the model 23.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4426 restraints for refining 2017 atoms. 4011 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2816 (Rfree = 0.000) for 2017 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 27: After refmac, R = 0.2878 (Rfree = 0.000) for 2019 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 28: After refmac, R = 0.2787 (Rfree = 0.000) for 2019 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.2330 (Rfree = 0.000) for 2022 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.2675 (Rfree = 0.000) for 2018 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 2088 seeds are put forward Round 1: 100 peptides, 17 chains. Longest chain 16 peptides. Score 0.395 Round 2: 116 peptides, 18 chains. Longest chain 17 peptides. Score 0.466 Round 3: 119 peptides, 18 chains. Longest chain 17 peptides. Score 0.483 Round 4: 117 peptides, 18 chains. Longest chain 18 peptides. Score 0.471 Round 5: 118 peptides, 17 chains. Longest chain 19 peptides. Score 0.502 Taking the results from Round 5 Chains 17, Residues 101, Estimated correctness of the model 12.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4265 restraints for refining 1977 atoms. 3859 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2725 (Rfree = 0.000) for 1977 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.2470 (Rfree = 0.000) for 1980 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.2683 (Rfree = 0.000) for 1983 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2323 (Rfree = 0.000) for 1985 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2171 (Rfree = 0.000) for 1992 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 2028 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 2063 seeds are put forward Round 1: 93 peptides, 17 chains. Longest chain 13 peptides. Score 0.349 Round 2: 107 peptides, 18 chains. Longest chain 16 peptides. Score 0.412 Round 3: 110 peptides, 17 chains. Longest chain 18 peptides. Score 0.456 Round 4: 117 peptides, 20 chains. Longest chain 17 peptides. Score 0.420 Round 5: 126 peptides, 19 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 5 Chains 21, Residues 107, Estimated correctness of the model 10.7 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4135 restraints for refining 1983 atoms. 3700 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2444 (Rfree = 0.000) for 1983 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 37: After refmac, R = 0.2348 (Rfree = 0.000) for 1988 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2350 (Rfree = 0.000) for 1991 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 39: After refmac, R = 0.2371 (Rfree = 0.000) for 1993 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2429 (Rfree = 0.000) for 1997 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 2045 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2057 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.316 Round 2: 108 peptides, 17 chains. Longest chain 13 peptides. Score 0.444 Round 3: 115 peptides, 20 chains. Longest chain 13 peptides. Score 0.408 Round 4: 114 peptides, 18 chains. Longest chain 11 peptides. Score 0.454 Round 5: 113 peptides, 17 chains. Longest chain 14 peptides. Score 0.474 Taking the results from Round 5 Chains 17, Residues 96, Estimated correctness of the model 2.7 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4183 restraints for refining 1988 atoms. 3766 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2680 (Rfree = 0.000) for 1988 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 42: After refmac, R = 0.2669 (Rfree = 0.000) for 1977 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2101 (Rfree = 0.000) for 1984 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.1948 (Rfree = 0.000) for 1980 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.2258 (Rfree = 0.000) for 1977 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 2017 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2031 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 9 peptides. Score 0.397 Round 2: 100 peptides, 16 chains. Longest chain 12 peptides. Score 0.422 Round 3: 105 peptides, 14 chains. Longest chain 16 peptides. Score 0.504 Round 4: 104 peptides, 14 chains. Longest chain 16 peptides. Score 0.499 Round 5: 108 peptides, 14 chains. Longest chain 17 peptides. Score 0.521 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 94, Estimated correctness of the model 18.0 % 5 chains (44 residues) have been docked in sequence Sequence coverage is 46 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 120 A and 125 A 15 chains (98 residues) following loop building 4 chains (48 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4668 reflections ( 99.79 % complete ) and 3902 restraints for refining 2043 atoms. 3361 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2557 (Rfree = 0.000) for 2043 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2595 (Rfree = 0.000) for 2024 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2693 (Rfree = 0.000) for 2010 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2768 (Rfree = 0.000) for 1993 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:06:32 GMT 2018 Job finished. TimeTaking 31.11 Used memory is bytes: 2369472