Mon 24 Dec 00:29:15 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 2ooj-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooj-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-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/2ooj-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-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 00:29:20 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/2ooj-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-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 193 and 0 Target number of residues in the AU: 193 Target solvent content: 0.6226 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 282 Adjusted target solvent content: 0.45 Input MTZ file: 2ooj-3.4-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: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2256 target number of atoms Had to go as low as 0.60 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: 53.043 3.400 Wilson plot Bfac: 61.81 4089 reflections ( 99.18 % complete ) and 0 restraints for refining 2498 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3492 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2745 (Rfree = 0.000) for 2498 atoms. Found 18 (18 requested) and removed 41 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 2502 seeds are put forward NCS extension: 0 residues added, 2502 seeds are put forward Round 1: 115 peptides, 22 chains. Longest chain 11 peptides. Score 0.344 Round 2: 132 peptides, 23 chains. Longest chain 11 peptides. Score 0.418 Round 3: 134 peptides, 20 chains. Longest chain 12 peptides. Score 0.499 Round 4: 157 peptides, 23 chains. Longest chain 16 peptides. Score 0.547 Round 5: 160 peptides, 22 chains. Longest chain 14 peptides. Score 0.580 Taking the results from Round 5 Chains 22, Residues 138, Estimated correctness of the model 22.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4751 restraints for refining 2051 atoms. 4221 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2743 (Rfree = 0.000) for 2051 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 2: After refmac, R = 0.2553 (Rfree = 0.000) for 2010 atoms. Found 9 (15 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.2756 (Rfree = 0.000) for 1992 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 4: After refmac, R = 0.2519 (Rfree = 0.000) for 1985 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2590 (Rfree = 0.000) for 1972 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2044 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 13 peptides. Score 0.418 Round 2: 146 peptides, 23 chains. Longest chain 15 peptides. Score 0.493 Round 3: 145 peptides, 21 chains. Longest chain 14 peptides. Score 0.531 Round 4: 150 peptides, 22 chains. Longest chain 16 peptides. Score 0.534 Round 5: 162 peptides, 24 chains. Longest chain 15 peptides. Score 0.550 Taking the results from Round 5 Chains 24, Residues 138, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4739 restraints for refining 2052 atoms. 4211 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2645 (Rfree = 0.000) for 2052 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 7: After refmac, R = 0.2559 (Rfree = 0.000) for 2044 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.2705 (Rfree = 0.000) for 2034 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.2384 (Rfree = 0.000) for 2027 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2495 (Rfree = 0.000) for 2019 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2069 seeds are put forward Round 1: 132 peptides, 22 chains. Longest chain 15 peptides. Score 0.442 Round 2: 138 peptides, 21 chains. Longest chain 16 peptides. Score 0.497 Round 3: 150 peptides, 25 chains. Longest chain 12 peptides. Score 0.469 Round 4: 143 peptides, 21 chains. Longest chain 16 peptides. Score 0.522 Round 5: 139 peptides, 18 chains. Longest chain 17 peptides. Score 0.566 Taking the results from Round 5 Chains 18, Residues 121, Estimated correctness of the model 17.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4901 restraints for refining 2052 atoms. 4435 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2733 (Rfree = 0.000) for 2052 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 12: After refmac, R = 0.2500 (Rfree = 0.000) for 2046 atoms. Found 10 (15 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.2443 (Rfree = 0.000) for 2039 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.2349 (Rfree = 0.000) for 2041 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.2001 (Rfree = 0.000) for 2043 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 2092 seeds are put forward Round 1: 131 peptides, 22 chains. Longest chain 12 peptides. Score 0.436 Round 2: 135 peptides, 18 chains. Longest chain 15 peptides. Score 0.547 Round 3: 140 peptides, 21 chains. Longest chain 15 peptides. Score 0.507 Round 4: 139 peptides, 20 chains. Longest chain 15 peptides. Score 0.524 Round 5: 149 peptides, 20 chains. Longest chain 20 peptides. Score 0.571 Taking the results from Round 5 Chains 20, Residues 129, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4714 restraints for refining 2045 atoms. 4218 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2340 (Rfree = 0.000) for 2045 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.2151 (Rfree = 0.000) for 2042 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.2123 (Rfree = 0.000) for 2030 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.2051 (Rfree = 0.000) for 2023 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.1998 (Rfree = 0.000) for 2015 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2055 seeds are put forward Round 1: 122 peptides, 20 chains. Longest chain 13 peptides. Score 0.435 Round 2: 120 peptides, 16 chains. Longest chain 11 peptides. Score 0.518 Round 3: 143 peptides, 18 chains. Longest chain 16 peptides. Score 0.584 Round 4: 143 peptides, 18 chains. Longest chain 19 peptides. Score 0.584 Round 5: 146 peptides, 18 chains. Longest chain 18 peptides. Score 0.598 Taking the results from Round 5 Chains 18, Residues 128, Estimated correctness of the model 28.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4639 restraints for refining 2030 atoms. 4145 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2366 (Rfree = 0.000) for 2030 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 22: After refmac, R = 0.2249 (Rfree = 0.000) for 2023 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 23: After refmac, R = 0.2176 (Rfree = 0.000) for 2019 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.2111 (Rfree = 0.000) for 2012 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.2056 (Rfree = 0.000) for 2005 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2055 seeds are put forward Round 1: 126 peptides, 17 chains. Longest chain 15 peptides. Score 0.525 Round 2: 136 peptides, 18 chains. Longest chain 13 peptides. Score 0.552 Round 3: 136 peptides, 20 chains. Longest chain 12 peptides. Score 0.509 Round 4: 136 peptides, 16 chains. Longest chain 20 peptides. Score 0.594 Round 5: 136 peptides, 19 chains. Longest chain 14 peptides. Score 0.531 Taking the results from Round 4 Chains 16, Residues 120, Estimated correctness of the model 26.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4749 restraints for refining 2041 atoms. 4285 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2284 (Rfree = 0.000) for 2041 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.2130 (Rfree = 0.000) for 2036 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.2054 (Rfree = 0.000) for 2030 atoms. Found 8 (15 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.2036 (Rfree = 0.000) for 2030 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.2017 (Rfree = 0.000) for 2026 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 2076 seeds are put forward Round 1: 122 peptides, 18 chains. Longest chain 18 peptides. Score 0.482 Round 2: 136 peptides, 19 chains. Longest chain 18 peptides. Score 0.531 Round 3: 134 peptides, 19 chains. Longest chain 17 peptides. Score 0.521 Round 4: 126 peptides, 18 chains. Longest chain 18 peptides. Score 0.503 Round 5: 129 peptides, 16 chains. Longest chain 21 peptides. Score 0.562 Taking the results from Round 5 Chains 18, Residues 113, Estimated correctness of the model 15.8 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4644 restraints for refining 2052 atoms. 4159 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2250 (Rfree = 0.000) for 2052 atoms. Found 9 (15 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.2251 (Rfree = 0.000) for 2043 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.2301 (Rfree = 0.000) for 2035 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1963 (Rfree = 0.000) for 2033 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1911 (Rfree = 0.000) for 2025 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2058 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2075 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.365 Round 2: 119 peptides, 19 chains. Longest chain 14 peptides. Score 0.442 Round 3: 138 peptides, 20 chains. Longest chain 14 peptides. Score 0.519 Round 4: 136 peptides, 20 chains. Longest chain 14 peptides. Score 0.509 Round 5: 136 peptides, 21 chains. Longest chain 14 peptides. Score 0.486 Taking the results from Round 3 Chains 21, Residues 118, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4522 restraints for refining 2052 atoms. 3987 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2442 (Rfree = 0.000) for 2052 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.2194 (Rfree = 0.000) for 2050 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.2207 (Rfree = 0.000) for 2053 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.2219 (Rfree = 0.000) for 2049 atoms. Found 7 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2194 (Rfree = 0.000) for 2046 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 2080 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2097 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.355 Round 2: 132 peptides, 21 chains. Longest chain 12 peptides. Score 0.465 Round 3: 140 peptides, 20 chains. Longest chain 13 peptides. Score 0.529 Round 4: 140 peptides, 21 chains. Longest chain 14 peptides. Score 0.507 Round 5: 132 peptides, 21 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 3 Chains 22, Residues 120, Estimated correctness of the model 3.8 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4494 restraints for refining 2052 atoms. 3970 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2130 (Rfree = 0.000) for 2052 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.2002 (Rfree = 0.000) for 2041 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.1988 (Rfree = 0.000) for 2036 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1953 (Rfree = 0.000) for 2030 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1938 (Rfree = 0.000) for 2026 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2063 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 11 peptides. Score 0.333 Round 2: 109 peptides, 16 chains. Longest chain 11 peptides. Score 0.460 Round 3: 116 peptides, 17 chains. Longest chain 11 peptides. Score 0.474 Round 4: 115 peptides, 16 chains. Longest chain 13 peptides. Score 0.492 Round 5: 107 peptides, 15 chains. Longest chain 11 peptides. Score 0.473 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 99, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2ooj-3_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (99 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4089 reflections ( 99.18 % complete ) and 4606 restraints for refining 2052 atoms. 4172 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2046 (Rfree = 0.000) for 2052 atoms. Found 0 (15 requested) and removed 2 (7 requested) atoms. Cycle 47: After refmac, R = 0.1980 (Rfree = 0.000) for 2043 atoms. Found 0 (15 requested) and removed 0 (7 requested) atoms. Cycle 48: After refmac, R = 0.1956 (Rfree = 0.000) for 2042 atoms. Found 0 (15 requested) and removed 2 (7 requested) atoms. Cycle 49: After refmac, R = 0.1954 (Rfree = 0.000) for 2040 atoms. TimeTaking 31.5