Mon 24 Dec 00:35:10 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 2gnr-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-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/2gnr-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-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 00:35:15 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/2gnr-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-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 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.6662 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: 0.52 Input MTZ file: 2gnr-3.8-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: 91 Cell parameters: 75.160 75.160 115.370 90.000 90.000 90.000 Input sequence file: 2gnr-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.70 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: 75.160 3.801 Wilson plot Bfac: 88.62 3561 reflections ( 99.30 % complete ) and 0 restraints for refining 2557 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3462 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3351 (Rfree = 0.000) for 2557 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 2589 seeds are put forward NCS extension: 0 residues added, 2589 seeds are put forward Round 1: 122 peptides, 21 chains. Longest chain 11 peptides. Score 0.382 Round 2: 148 peptides, 22 chains. Longest chain 15 peptides. Score 0.485 Round 3: 165 peptides, 24 chains. Longest chain 13 peptides. Score 0.521 Round 4: 163 peptides, 23 chains. Longest chain 19 peptides. Score 0.531 Round 5: 176 peptides, 22 chains. Longest chain 22 peptides. Score 0.599 Taking the results from Round 5 Chains 23, Residues 154, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4674 restraints for refining 2098 atoms. 4046 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2591 (Rfree = 0.000) for 2098 atoms. Found 6 (11 requested) and removed 12 (5 requested) atoms. Cycle 2: After refmac, R = 0.2620 (Rfree = 0.000) for 2039 atoms. Found 7 (11 requested) and removed 16 (5 requested) atoms. Cycle 3: After refmac, R = 0.2376 (Rfree = 0.000) for 2010 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2305 (Rfree = 0.000) for 1997 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2217 (Rfree = 0.000) for 1987 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 2063 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2092 seeds are put forward Round 1: 149 peptides, 26 chains. Longest chain 10 peptides. Score 0.409 Round 2: 161 peptides, 22 chains. Longest chain 22 peptides. Score 0.541 Round 3: 165 peptides, 21 chains. Longest chain 24 peptides. Score 0.574 Round 4: 165 peptides, 23 chains. Longest chain 19 peptides. Score 0.539 Round 5: 170 peptides, 20 chains. Longest chain 26 peptides. Score 0.610 Taking the results from Round 5 Chains 20, Residues 150, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4566 restraints for refining 2057 atoms. 3986 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2359 (Rfree = 0.000) for 2057 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. Cycle 7: After refmac, R = 0.2219 (Rfree = 0.000) for 2038 atoms. Found 8 (11 requested) and removed 17 (5 requested) atoms. Cycle 8: After refmac, R = 0.2122 (Rfree = 0.000) for 2021 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.2153 (Rfree = 0.000) for 2014 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.2009 (Rfree = 0.000) for 2006 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 2069 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2097 seeds are put forward Round 1: 144 peptides, 22 chains. Longest chain 15 peptides. Score 0.467 Round 2: 145 peptides, 20 chains. Longest chain 13 peptides. Score 0.511 Round 3: 154 peptides, 16 chains. Longest chain 28 peptides. Score 0.619 Round 4: 157 peptides, 17 chains. Longest chain 29 peptides. Score 0.613 Round 5: 165 peptides, 20 chains. Longest chain 33 peptides. Score 0.592 Taking the results from Round 3 Chains 16, Residues 138, Estimated correctness of the model 7.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4731 restraints for refining 2097 atoms. 4195 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2077 (Rfree = 0.000) for 2097 atoms. Found 3 (11 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.2079 (Rfree = 0.000) for 2081 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. Cycle 13: After refmac, R = 0.2020 (Rfree = 0.000) for 2071 atoms. Found 8 (11 requested) and removed 11 (5 requested) atoms. Cycle 14: After refmac, R = 0.2247 (Rfree = 0.000) for 2067 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 15: After refmac, R = 0.2058 (Rfree = 0.000) for 2061 atoms. Found 11 (11 requested) and removed 35 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 2091 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 2133 seeds are put forward Round 1: 127 peptides, 25 chains. Longest chain 11 peptides. Score 0.320 Round 2: 136 peptides, 18 chains. Longest chain 19 peptides. Score 0.511 Round 3: 140 peptides, 20 chains. Longest chain 18 peptides. Score 0.489 Round 4: 143 peptides, 19 chains. Longest chain 14 peptides. Score 0.522 Round 5: 148 peptides, 18 chains. Longest chain 31 peptides. Score 0.561 Taking the results from Round 5 Chains 18, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4877 restraints for refining 2098 atoms. 4375 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2797 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 17: After refmac, R = 0.2565 (Rfree = 0.000) for 2066 atoms. Found 9 (11 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.2331 (Rfree = 0.000) for 2058 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.2283 (Rfree = 0.000) for 2051 atoms. Found 10 (11 requested) and removed 21 (5 requested) atoms. Cycle 20: After refmac, R = 0.2265 (Rfree = 0.000) for 2038 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 2111 seeds are put forward NCS extension: 42 residues added (4 deleted due to clashes), 2153 seeds are put forward Round 1: 110 peptides, 22 chains. Longest chain 10 peptides. Score 0.296 Round 2: 140 peptides, 21 chains. Longest chain 12 peptides. Score 0.469 Round 3: 138 peptides, 24 chains. Longest chain 12 peptides. Score 0.398 Round 4: 152 peptides, 23 chains. Longest chain 19 peptides. Score 0.484 Round 5: 153 peptides, 24 chains. Longest chain 26 peptides. Score 0.468 Taking the results from Round 4 Chains 23, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4950 restraints for refining 2098 atoms. 4457 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2661 (Rfree = 0.000) for 2098 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 22: After refmac, R = 0.2279 (Rfree = 0.000) for 2076 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.2265 (Rfree = 0.000) for 2061 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2188 (Rfree = 0.000) for 2051 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1926 (Rfree = 0.000) for 2045 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 2109 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 2138 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.297 Round 2: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.417 Round 3: 128 peptides, 19 chains. Longest chain 14 peptides. Score 0.455 Round 4: 126 peptides, 17 chains. Longest chain 25 peptides. Score 0.487 Round 5: 135 peptides, 14 chains. Longest chain 25 peptides. Score 0.583 Taking the results from Round 5 Chains 14, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4845 restraints for refining 2098 atoms. 4375 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2234 (Rfree = 0.000) for 2098 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. Cycle 27: After refmac, R = 0.2301 (Rfree = 0.000) for 2087 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 28: After refmac, R = 0.2180 (Rfree = 0.000) for 2080 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 29: After refmac, R = 0.2381 (Rfree = 0.000) for 2075 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.2245 (Rfree = 0.000) for 2064 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.55 Search for helices and strands: 0 residues in 0 chains, 2124 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2150 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 8 peptides. Score 0.263 Round 2: 117 peptides, 20 chains. Longest chain 11 peptides. Score 0.379 Round 3: 122 peptides, 20 chains. Longest chain 12 peptides. Score 0.404 Round 4: 117 peptides, 19 chains. Longest chain 14 peptides. Score 0.401 Round 5: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 20, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4975 restraints for refining 2098 atoms. 4579 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2471 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 33 (5 requested) atoms. Cycle 32: After refmac, R = 0.2228 (Rfree = 0.000) for 2064 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 33: After refmac, R = 0.2108 (Rfree = 0.000) for 2059 atoms. Found 8 (11 requested) and removed 13 (5 requested) atoms. Cycle 34: After refmac, R = 0.2156 (Rfree = 0.000) for 2048 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. Cycle 35: After refmac, R = 0.2080 (Rfree = 0.000) for 2036 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2131 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 8 peptides. Score 0.252 Round 2: 114 peptides, 20 chains. Longest chain 10 peptides. Score 0.363 Round 3: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.326 Round 4: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.355 Round 5: 118 peptides, 16 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 5 Chains 16, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4847 restraints for refining 2098 atoms. 4455 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2485 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 37: After refmac, R = 0.2667 (Rfree = 0.000) for 2078 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 38: After refmac, R = 0.2136 (Rfree = 0.000) for 2070 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 39: After refmac, R = 0.2097 (Rfree = 0.000) for 2061 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.1731 (Rfree = 0.000) for 2053 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.55 Search for helices and strands: 0 residues in 0 chains, 2106 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2123 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.296 Round 2: 96 peptides, 17 chains. Longest chain 13 peptides. Score 0.337 Round 3: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.369 Round 4: 110 peptides, 15 chains. Longest chain 16 peptides. Score 0.455 Round 5: 120 peptides, 16 chains. Longest chain 13 peptides. Score 0.480 Taking the results from Round 5 Chains 16, Residues 104, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4733 restraints for refining 2098 atoms. 4304 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2450 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 42: After refmac, R = 0.2205 (Rfree = 0.000) for 2081 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.2049 (Rfree = 0.000) for 2072 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.2150 (Rfree = 0.000) for 2065 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2058 (Rfree = 0.000) for 2062 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 2130 seeds are put forward NCS extension: 0 residues added, 2130 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 8 peptides. Score 0.246 Round 2: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.333 Round 3: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.376 Round 4: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.351 Round 5: 119 peptides, 19 chains. Longest chain 10 peptides. Score 0.411 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gnr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3561 reflections ( 99.30 % complete ) and 4862 restraints for refining 2098 atoms. 4481 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2276 (Rfree = 0.000) for 2098 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2198 (Rfree = 0.000) for 2086 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2134 (Rfree = 0.000) for 2076 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2160 (Rfree = 0.000) for 2063 atoms. TimeTaking 32.88