Sun 23 Dec 22:22:53 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.6-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 22:23:03 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.6-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.6562 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 81.53 3840 reflections ( 99.43 % complete ) and 0 restraints for refining 2719 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3537 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3040 (Rfree = 0.000) for 2719 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.82 Search for helices and strands: 0 residues in 0 chains, 2796 seeds are put forward NCS extension: 0 residues added, 2796 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 6 peptides. Score 0.249 Round 2: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.358 Round 3: 131 peptides, 20 chains. Longest chain 13 peptides. Score 0.460 Round 4: 119 peptides, 18 chains. Longest chain 16 peptides. Score 0.444 Round 5: 125 peptides, 19 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 3 Chains 20, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5372 restraints for refining 2228 atoms. 4948 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2419 (Rfree = 0.000) for 2228 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 2: After refmac, R = 0.2379 (Rfree = 0.000) for 2191 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 3: After refmac, R = 0.1814 (Rfree = 0.000) for 2180 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 4: After refmac, R = 0.1705 (Rfree = 0.000) for 2171 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.1657 (Rfree = 0.000) for 2161 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 2280 seeds are put forward NCS extension: 0 residues added, 2280 seeds are put forward Round 1: 104 peptides, 23 chains. Longest chain 7 peptides. Score 0.242 Round 2: 119 peptides, 21 chains. Longest chain 12 peptides. Score 0.376 Round 3: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.355 Round 4: 126 peptides, 20 chains. Longest chain 13 peptides. Score 0.435 Round 5: 117 peptides, 18 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 4 Chains 20, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4928 restraints for refining 2100 atoms. 4524 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2166 (Rfree = 0.000) for 2100 atoms. Found 7 (13 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.1943 (Rfree = 0.000) for 2076 atoms. Found 5 (13 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.2066 (Rfree = 0.000) for 2043 atoms. Found 7 (13 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2442 (Rfree = 0.000) for 2022 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 10: After refmac, R = 0.2444 (Rfree = 0.000) for 2014 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2147 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2166 seeds are put forward Round 1: 115 peptides, 22 chains. Longest chain 10 peptides. Score 0.330 Round 2: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.367 Round 3: 128 peptides, 23 chains. Longest chain 10 peptides. Score 0.378 Round 4: 135 peptides, 21 chains. Longest chain 13 peptides. Score 0.458 Round 5: 137 peptides, 22 chains. Longest chain 12 peptides. Score 0.446 Taking the results from Round 4 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4684 restraints for refining 2068 atoms. 4249 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2018 (Rfree = 0.000) for 2068 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 12: After refmac, R = 0.2481 (Rfree = 0.000) for 2052 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.2060 (Rfree = 0.000) for 2038 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.1738 (Rfree = 0.000) for 2025 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.1742 (Rfree = 0.000) for 2018 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.69 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 0 residues added, 2123 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.285 Round 2: 139 peptides, 22 chains. Longest chain 18 peptides. Score 0.456 Round 3: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.367 Round 4: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.367 Round 5: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.336 Taking the results from Round 2 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4459 restraints for refining 2013 atoms. 4013 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1996 (Rfree = 0.000) for 2013 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 17: After refmac, R = 0.1650 (Rfree = 0.000) for 2005 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.1915 (Rfree = 0.000) for 1997 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.1881 (Rfree = 0.000) for 1998 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1749 (Rfree = 0.000) for 1993 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.67 Search for helices and strands: 0 residues in 0 chains, 2104 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2128 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 9 peptides. Score 0.275 Round 2: 115 peptides, 19 chains. Longest chain 16 peptides. Score 0.401 Round 3: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.408 Round 4: 115 peptides, 18 chains. Longest chain 16 peptides. Score 0.424 Round 5: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 4 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4557 restraints for refining 2031 atoms. 4187 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1954 (Rfree = 0.000) for 2031 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.1745 (Rfree = 0.000) for 2023 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 23: After refmac, R = 0.1661 (Rfree = 0.000) for 2018 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1660 (Rfree = 0.000) for 2018 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1580 (Rfree = 0.000) for 2018 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2129 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2151 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.249 Round 2: 112 peptides, 20 chains. Longest chain 14 peptides. Score 0.361 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.379 Round 4: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.385 Round 5: 120 peptides, 18 chains. Longest chain 16 peptides. Score 0.449 Taking the results from Round 5 Chains 18, Residues 102, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4820 restraints for refining 2159 atoms. 4372 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2049 (Rfree = 0.000) for 2159 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 27: After refmac, R = 0.1885 (Rfree = 0.000) for 2143 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.1882 (Rfree = 0.000) for 2137 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.1833 (Rfree = 0.000) for 2132 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.1875 (Rfree = 0.000) for 2129 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2226 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2242 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 8 peptides. Score 0.254 Round 2: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.356 Round 3: 97 peptides, 16 chains. Longest chain 16 peptides. Score 0.375 Round 4: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.391 Round 5: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.352 Taking the results from Round 4 Chains 14, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4842 restraints for refining 2096 atoms. 4548 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1986 (Rfree = 0.000) for 2096 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.2037 (Rfree = 0.000) for 2093 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.1523 (Rfree = 0.000) for 2092 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1434 (Rfree = 0.000) for 2088 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1396 (Rfree = 0.000) for 2081 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2176 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2195 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 6 peptides. Score 0.234 Round 2: 101 peptides, 19 chains. Longest chain 13 peptides. Score 0.323 Round 3: 107 peptides, 21 chains. Longest chain 8 peptides. Score 0.309 Round 4: 104 peptides, 18 chains. Longest chain 15 peptides. Score 0.365 Round 5: 103 peptides, 18 chains. Longest chain 15 peptides. Score 0.359 Taking the results from Round 4 Chains 18, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 4985 restraints for refining 2114 atoms. 4659 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1878 (Rfree = 0.000) for 2114 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.1993 (Rfree = 0.000) for 2113 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 38: After refmac, R = 0.1632 (Rfree = 0.000) for 2108 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1610 (Rfree = 0.000) for 2100 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1569 (Rfree = 0.000) for 2097 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward NCS extension: 0 residues added, 2193 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 7 peptides. Score 0.264 Round 2: 90 peptides, 16 chains. Longest chain 8 peptides. Score 0.335 Round 3: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.329 Round 4: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.375 Round 5: 96 peptides, 17 chains. Longest chain 11 peptides. Score 0.344 Taking the results from Round 4 Chains 16, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3840 reflections ( 99.43 % complete ) and 5052 restraints for refining 2144 atoms. 4744 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2009 (Rfree = 0.000) for 2144 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 42: After refmac, R = 0.2059 (Rfree = 0.000) for 2131 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.1929 (Rfree = 0.000) for 2130 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.1591 (Rfree = 0.000) for 2131 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.1524 (Rfree = 0.000) for 2128 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward NCS extension: 0 residues added, 2202 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.216 Round 2: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.323 Round 3: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.303 Round 4: 88 peptides, 14 chains. Longest chain 19 peptides. Score 0.374 Round 5: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 74, 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. 3840 reflections ( 99.43 % complete ) and 5045 restraints for refining 2147 atoms. 4763 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2111 (Rfree = 0.000) for 2147 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1939 (Rfree = 0.000) for 2137 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1944 (Rfree = 0.000) for 2126 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1879 (Rfree = 0.000) for 2117 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 33.9