Mon 24 Dec 07:38:56 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 2p1a-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-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/2p1a-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-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 07:39:01 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/2p1a-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-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 190 and 0 Target number of residues in the AU: 190 Target solvent content: 0.6650 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-3.8-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: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 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: 29.570 3.800 Wilson plot Bfac: 87.77 3278 reflections ( 99.42 % complete ) and 0 restraints for refining 2729 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3624 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3578 (Rfree = 0.000) for 2729 atoms. Found 15 (15 requested) and removed 39 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.87 4.08 Search for helices and strands: 0 residues in 0 chains, 2780 seeds are put forward NCS extension: 0 residues added, 2780 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 6 peptides. Score 0.196 Round 2: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.260 Round 3: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.335 Round 4: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.346 Round 5: 113 peptides, 17 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 5 Chains 17, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5556 restraints for refining 2229 atoms. 5189 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2850 (Rfree = 0.000) for 2229 atoms. Found 9 (12 requested) and removed 23 (6 requested) atoms. Cycle 2: After refmac, R = 0.2492 (Rfree = 0.000) for 2178 atoms. Found 11 (12 requested) and removed 21 (6 requested) atoms. Cycle 3: After refmac, R = 0.2340 (Rfree = 0.000) for 2145 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Cycle 4: After refmac, R = 0.2120 (Rfree = 0.000) for 2118 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2039 (Rfree = 0.000) for 2109 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.90 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2245 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 7 peptides. Score 0.263 Round 2: 104 peptides, 16 chains. Longest chain 16 peptides. Score 0.413 Round 3: 104 peptides, 18 chains. Longest chain 9 peptides. Score 0.365 Round 4: 113 peptides, 18 chains. Longest chain 11 peptides. Score 0.413 Round 5: 113 peptides, 16 chains. Longest chain 21 peptides. Score 0.459 Taking the results from Round 5 Chains 16, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4921 restraints for refining 2090 atoms. 4549 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2204 (Rfree = 0.000) for 2090 atoms. Found 9 (11 requested) and removed 17 (5 requested) atoms. Cycle 7: After refmac, R = 0.1942 (Rfree = 0.000) for 2067 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1840 (Rfree = 0.000) for 2063 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.1809 (Rfree = 0.000) for 2056 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1719 (Rfree = 0.000) for 2056 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.87 Search for helices and strands: 0 residues in 0 chains, 2155 seeds are put forward NCS extension: 0 residues added, 2155 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.276 Round 2: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.387 Round 3: 107 peptides, 18 chains. Longest chain 10 peptides. Score 0.381 Round 4: 111 peptides, 18 chains. Longest chain 10 peptides. Score 0.403 Round 5: 117 peptides, 20 chains. Longest chain 9 peptides. Score 0.388 Taking the results from Round 4 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4833 restraints for refining 2113 atoms. 4479 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2236 (Rfree = 0.000) for 2113 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.2064 (Rfree = 0.000) for 2084 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.1662 (Rfree = 0.000) for 2071 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.1729 (Rfree = 0.000) for 2064 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.1568 (Rfree = 0.000) for 2060 atoms. Found 2 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2177 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2185 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 9 peptides. Score 0.270 Round 2: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.386 Round 3: 115 peptides, 18 chains. Longest chain 14 peptides. Score 0.424 Round 4: 127 peptides, 19 chains. Longest chain 16 peptides. Score 0.462 Round 5: 124 peptides, 17 chains. Longest chain 16 peptides. Score 0.490 Taking the results from Round 5 Chains 17, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4965 restraints for refining 2156 atoms. 4554 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2098 (Rfree = 0.000) for 2156 atoms. Found 10 (11 requested) and removed 15 (5 requested) atoms. Cycle 17: After refmac, R = 0.2037 (Rfree = 0.000) for 2142 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.2071 (Rfree = 0.000) for 2135 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.2049 (Rfree = 0.000) for 2126 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.1864 (Rfree = 0.000) for 2122 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 2249 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.296 Round 2: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.389 Round 3: 99 peptides, 14 chains. Longest chain 12 peptides. Score 0.434 Round 4: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.378 Round 5: 101 peptides, 14 chains. Longest chain 15 peptides. Score 0.444 Taking the results from Round 5 Chains 14, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5066 restraints for refining 2136 atoms. 4732 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2019 (Rfree = 0.000) for 2136 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 22: After refmac, R = 0.1897 (Rfree = 0.000) for 2125 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.1616 (Rfree = 0.000) for 2123 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.1617 (Rfree = 0.000) for 2115 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1556 (Rfree = 0.000) for 2110 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 2216 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2231 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.294 Round 2: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.379 Round 3: 108 peptides, 20 chains. Longest chain 12 peptides. Score 0.339 Round 4: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.356 Round 5: 114 peptides, 19 chains. Longest chain 13 peptides. Score 0.395 Taking the results from Round 5 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5227 restraints for refining 2228 atoms. 4866 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2200 (Rfree = 0.000) for 2228 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.2141 (Rfree = 0.000) for 2213 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.1897 (Rfree = 0.000) for 2200 atoms. Found 7 (12 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.1966 (Rfree = 0.000) for 2192 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.1933 (Rfree = 0.000) for 2184 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.92 Search for helices and strands: 0 residues in 0 chains, 2290 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2305 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.238 Round 2: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 3: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.323 Round 4: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.346 Round 5: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.297 Taking the results from Round 4 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5297 restraints for refining 2205 atoms. 5009 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2022 (Rfree = 0.000) for 2205 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.1880 (Rfree = 0.000) for 2196 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.2101 (Rfree = 0.000) for 2185 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.2178 (Rfree = 0.000) for 2178 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 35: After refmac, R = 0.2015 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.85 Search for helices and strands: 0 residues in 0 chains, 2270 seeds are put forward NCS extension: 0 residues added, 2270 seeds are put forward Round 1: 85 peptides, 20 chains. Longest chain 7 peptides. Score 0.200 Round 2: 89 peptides, 19 chains. Longest chain 6 peptides. Score 0.251 Round 3: 85 peptides, 16 chains. Longest chain 10 peptides. Score 0.305 Round 4: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 5: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.301 Taking the results from Round 3 Chains 16, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5046 restraints for refining 2132 atoms. 4786 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2005 (Rfree = 0.000) for 2132 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 37: After refmac, R = 0.1739 (Rfree = 0.000) for 2120 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.1643 (Rfree = 0.000) for 2122 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.1657 (Rfree = 0.000) for 2117 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.1666 (Rfree = 0.000) for 2112 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2194 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 2196 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.207 Round 2: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.299 Round 3: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.315 Round 4: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Round 5: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 5 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5180 restraints for refining 2139 atoms. 4956 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2426 (Rfree = 0.000) for 2139 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 42: After refmac, R = 0.2217 (Rfree = 0.000) for 2125 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.1817 (Rfree = 0.000) for 2121 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.1690 (Rfree = 0.000) for 2118 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.1685 (Rfree = 0.000) for 2113 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.90 Search for helices and strands: 0 residues in 0 chains, 2194 seeds are put forward NCS extension: 0 residues added, 2194 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.184 Round 2: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.201 Round 3: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.237 Round 4: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.268 Round 5: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.299 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 51, 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 2p1a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3278 reflections ( 99.42 % complete ) and 5055 restraints for refining 2139 atoms. 4862 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1827 (Rfree = 0.000) for 2139 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1756 (Rfree = 0.000) for 2131 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1892 (Rfree = 0.000) for 2124 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2107 (Rfree = 0.000) for 2115 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 28