Sun 23 Dec 22:22:42 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p1a-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:43 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/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.8-parrot-hancs/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-hancs.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-hancs.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 2722 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3599 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3428 (Rfree = 0.000) for 2722 atoms. Found 14 (14 requested) and removed 38 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 4.00 Search for helices and strands: 0 residues in 0 chains, 2773 seeds are put forward NCS extension: 0 residues added, 2773 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.262 Round 2: 102 peptides, 17 chains. Longest chain 14 peptides. Score 0.378 Round 3: 106 peptides, 15 chains. Longest chain 15 peptides. Score 0.446 Round 4: 108 peptides, 15 chains. Longest chain 15 peptides. Score 0.456 Round 5: 116 peptides, 16 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 5 Chains 16, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5473 restraints for refining 2229 atoms. 5089 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2443 (Rfree = 0.000) for 2229 atoms. Found 7 (12 requested) and removed 20 (6 requested) atoms. Cycle 2: After refmac, R = 0.2298 (Rfree = 0.000) for 2189 atoms. Found 6 (12 requested) and removed 15 (6 requested) atoms. Cycle 3: After refmac, R = 0.1915 (Rfree = 0.000) for 2169 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.1792 (Rfree = 0.000) for 2155 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.1761 (Rfree = 0.000) for 2148 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2249 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2263 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.249 Round 2: 129 peptides, 22 chains. Longest chain 12 peptides. Score 0.406 Round 3: 132 peptides, 24 chains. Longest chain 11 peptides. Score 0.377 Round 4: 136 peptides, 24 chains. Longest chain 12 peptides. Score 0.397 Round 5: 124 peptides, 20 chains. Longest chain 21 peptides. Score 0.425 Taking the results from Round 5 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4780 restraints for refining 2110 atoms. 4304 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2067 (Rfree = 0.000) for 2110 atoms. Found 6 (11 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.1905 (Rfree = 0.000) for 2082 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.1876 (Rfree = 0.000) for 2074 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 9: After refmac, R = 0.1927 (Rfree = 0.000) for 2063 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2093 (Rfree = 0.000) for 2054 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.92 Search for helices and strands: 0 residues in 0 chains, 2183 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2202 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 8 peptides. Score 0.291 Round 2: 132 peptides, 20 chains. Longest chain 15 peptides. Score 0.465 Round 3: 127 peptides, 20 chains. Longest chain 12 peptides. Score 0.440 Round 4: 124 peptides, 19 chains. Longest chain 13 peptides. Score 0.447 Round 5: 123 peptides, 19 chains. Longest chain 16 peptides. Score 0.442 Taking the results from Round 2 Chains 20, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4756 restraints for refining 2077 atoms. 4328 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 2077 atoms. Found 4 (11 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.2189 (Rfree = 0.000) for 2056 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.1875 (Rfree = 0.000) for 2048 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.1585 (Rfree = 0.000) for 2039 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.1540 (Rfree = 0.000) for 2036 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 2155 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 2168 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.299 Round 2: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.335 Round 3: 125 peptides, 23 chains. Longest chain 8 peptides. Score 0.362 Round 4: 111 peptides, 19 chains. Longest chain 9 peptides. Score 0.379 Round 5: 122 peptides, 21 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 5 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4977 restraints for refining 2130 atoms. 4594 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1947 (Rfree = 0.000) for 2130 atoms. Found 10 (11 requested) and removed 17 (5 requested) atoms. Cycle 17: After refmac, R = 0.2066 (Rfree = 0.000) for 2109 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.1899 (Rfree = 0.000) for 2104 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.1961 (Rfree = 0.000) for 2099 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 20: After refmac, R = 0.1777 (Rfree = 0.000) for 2091 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.87 Search for helices and strands: 0 residues in 0 chains, 2204 seeds are put forward NCS extension: 0 residues added, 2204 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 8 peptides. Score 0.296 Round 2: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.395 Round 3: 139 peptides, 23 chains. Longest chain 10 peptides. Score 0.435 Round 4: 133 peptides, 22 chains. Longest chain 10 peptides. Score 0.426 Round 5: 139 peptides, 22 chains. Longest chain 10 peptides. Score 0.456 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4936 restraints for refining 2162 atoms. 4490 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2033 (Rfree = 0.000) for 2162 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.1965 (Rfree = 0.000) for 2138 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2013 (Rfree = 0.000) for 2121 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 24: After refmac, R = 0.1898 (Rfree = 0.000) for 2107 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.1766 (Rfree = 0.000) for 2099 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.89 Search for helices and strands: 0 residues in 0 chains, 2235 seeds are put forward NCS extension: 0 residues added, 2235 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.261 Round 2: 117 peptides, 22 chains. Longest chain 11 peptides. Score 0.341 Round 3: 118 peptides, 23 chains. Longest chain 8 peptides. Score 0.323 Round 4: 129 peptides, 19 chains. Longest chain 18 peptides. Score 0.471 Round 5: 124 peptides, 21 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 4 Chains 19, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4825 restraints for refining 2106 atoms. 4404 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1968 (Rfree = 0.000) for 2106 atoms. Found 8 (11 requested) and removed 15 (5 requested) atoms. Cycle 27: After refmac, R = 0.1798 (Rfree = 0.000) for 2092 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1703 (Rfree = 0.000) for 2084 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1569 (Rfree = 0.000) for 2078 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1539 (Rfree = 0.000) for 2074 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.92 Search for helices and strands: 0 residues in 0 chains, 2166 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2192 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 9 peptides. Score 0.283 Round 2: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.321 Round 3: 100 peptides, 18 chains. Longest chain 17 peptides. Score 0.342 Round 4: 99 peptides, 17 chains. Longest chain 11 peptides. Score 0.361 Round 5: 99 peptides, 16 chains. Longest chain 14 peptides. Score 0.386 Taking the results from Round 5 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 5231 restraints for refining 2154 atoms. 4915 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2092 (Rfree = 0.000) for 2154 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2012 (Rfree = 0.000) for 2144 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.1562 (Rfree = 0.000) for 2137 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.1987 (Rfree = 0.000) for 2130 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.1437 (Rfree = 0.000) for 2130 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.86 Search for helices and strands: 0 residues in 0 chains, 2222 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2244 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.245 Round 2: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.310 Round 3: 112 peptides, 20 chains. Longest chain 12 peptides. Score 0.361 Round 4: 119 peptides, 20 chains. Longest chain 13 peptides. Score 0.399 Round 5: 121 peptides, 23 chains. Longest chain 13 peptides. Score 0.340 Taking the results from Round 4 Chains 20, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3278 reflections ( 99.42 % complete ) and 4958 restraints for refining 2129 atoms. 4582 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2006 (Rfree = 0.000) for 2129 atoms. Found 9 (11 requested) and removed 11 (5 requested) atoms. Cycle 37: After refmac, R = 0.2118 (Rfree = 0.000) for 2121 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 38: After refmac, R = 0.1708 (Rfree = 0.000) for 2116 atoms. Found 3 (11 requested) and removed 13 (5 requested) atoms. Cycle 39: After refmac, R = 0.1854 (Rfree = 0.000) for 2101 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.1592 (Rfree = 0.000) for 2103 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.90 Search for helices and strands: 0 residues in 0 chains, 2201 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2221 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.241 Round 2: 90 peptides, 18 chains. Longest chain 12 peptides. Score 0.283 Round 3: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.299 Round 4: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.291 Round 5: 88 peptides, 16 chains. Longest chain 13 peptides. Score 0.323 Taking the results from Round 5 Chains 16, Residues 72, 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 2134 atoms. 4794 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 2134 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. Cycle 42: After refmac, R = 0.1695 (Rfree = 0.000) for 2117 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.1622 (Rfree = 0.000) for 2105 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1658 (Rfree = 0.000) for 2091 atoms. Found 0 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.1648 (Rfree = 0.000) for 2083 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2174 seeds are put forward NCS extension: 0 residues added, 2174 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.236 Round 2: 76 peptides, 14 chains. Longest chain 12 peptides. Score 0.303 Round 3: 70 peptides, 13 chains. Longest chain 11 peptides. Score 0.293 Round 4: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.272 Round 5: 81 peptides, 14 chains. Longest chain 13 peptides. Score 0.333 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 67, 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 4959 restraints for refining 2093 atoms. 4705 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1918 (Rfree = 0.000) for 2093 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2145 (Rfree = 0.000) for 2081 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1805 (Rfree = 0.000) for 2064 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1619 (Rfree = 0.000) for 2055 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 77.58