Sun 23 Dec 22:23:01 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 2pr7-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.4-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/2pr7-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.4-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 22:23:11 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/2pr7-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-3.4-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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6408 Checking the provided sequence file Detected sequence length: 137 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 274 Adjusted target solvent content: 0.49 Input MTZ file: 2pr7-3.4-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: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.65 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: 57.053 3.400 Wilson plot Bfac: 71.78 3781 reflections ( 97.05 % complete ) and 0 restraints for refining 2435 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3071 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2874 (Rfree = 0.000) for 2435 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 2481 seeds are put forward NCS extension: 0 residues added, 2481 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 8 peptides. Score 0.299 Round 2: 133 peptides, 24 chains. Longest chain 9 peptides. Score 0.390 Round 3: 152 peptides, 23 chains. Longest chain 13 peptides. Score 0.509 Round 4: 154 peptides, 23 chains. Longest chain 12 peptides. Score 0.518 Round 5: 151 peptides, 22 chains. Longest chain 13 peptides. Score 0.525 Taking the results from Round 5 Chains 22, Residues 129, Estimated correctness of the model 2.3 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4293 restraints for refining 1991 atoms. 3735 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2259 (Rfree = 0.000) for 1991 atoms. Found 10 (15 requested) and removed 23 (7 requested) atoms. Cycle 2: After refmac, R = 0.2161 (Rfree = 0.000) for 1963 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2183 (Rfree = 0.000) for 1951 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 4: After refmac, R = 0.2168 (Rfree = 0.000) for 1944 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2147 (Rfree = 0.000) for 1939 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.38 Search for helices and strands: 0 residues in 0 chains, 2037 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2051 seeds are put forward Round 1: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.413 Round 2: 146 peptides, 21 chains. Longest chain 14 peptides. Score 0.522 Round 3: 147 peptides, 24 chains. Longest chain 12 peptides. Score 0.463 Round 4: 158 peptides, 25 chains. Longest chain 15 peptides. Score 0.496 Round 5: 165 peptides, 21 chains. Longest chain 17 peptides. Score 0.604 Taking the results from Round 5 Chains 22, Residues 144, Estimated correctness of the model 30.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4331 restraints for refining 1993 atoms. 3737 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2285 (Rfree = 0.000) for 1993 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 7: After refmac, R = 0.2067 (Rfree = 0.000) for 1985 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 8: After refmac, R = 0.2007 (Rfree = 0.000) for 1980 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 9: After refmac, R = 0.1960 (Rfree = 0.000) for 1974 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1934 (Rfree = 0.000) for 1968 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2072 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 11 peptides. Score 0.372 Round 2: 145 peptides, 23 chains. Longest chain 13 peptides. Score 0.475 Round 3: 142 peptides, 20 chains. Longest chain 13 peptides. Score 0.524 Round 4: 145 peptides, 21 chains. Longest chain 16 peptides. Score 0.517 Round 5: 140 peptides, 19 chains. Longest chain 16 peptides. Score 0.535 Taking the results from Round 5 Chains 19, Residues 121, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4533 restraints for refining 1992 atoms. 4068 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2185 (Rfree = 0.000) for 1992 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 12: After refmac, R = 0.2020 (Rfree = 0.000) for 1992 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 13: After refmac, R = 0.1954 (Rfree = 0.000) for 1985 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.1914 (Rfree = 0.000) for 1984 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.1910 (Rfree = 0.000) for 1976 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 2053 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2073 seeds are put forward Round 1: 128 peptides, 24 chains. Longest chain 9 peptides. Score 0.362 Round 2: 136 peptides, 18 chains. Longest chain 18 peptides. Score 0.538 Round 3: 137 peptides, 19 chains. Longest chain 17 peptides. Score 0.521 Round 4: 143 peptides, 19 chains. Longest chain 17 peptides. Score 0.549 Round 5: 141 peptides, 18 chains. Longest chain 15 peptides. Score 0.560 Taking the results from Round 5 Chains 18, Residues 123, Estimated correctness of the model 15.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4613 restraints for refining 1993 atoms. 4139 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2055 (Rfree = 0.000) for 1993 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 17: After refmac, R = 0.1918 (Rfree = 0.000) for 1989 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.1894 (Rfree = 0.000) for 1983 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.1862 (Rfree = 0.000) for 1980 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1844 (Rfree = 0.000) for 1975 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 2063 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2084 seeds are put forward Round 1: 124 peptides, 21 chains. Longest chain 11 peptides. Score 0.411 Round 2: 133 peptides, 21 chains. Longest chain 12 peptides. Score 0.458 Round 3: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.431 Round 4: 142 peptides, 21 chains. Longest chain 11 peptides. Score 0.503 Round 5: 138 peptides, 21 chains. Longest chain 10 peptides. Score 0.483 Taking the results from Round 4 Chains 21, Residues 121, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4524 restraints for refining 1993 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1951 (Rfree = 0.000) for 1993 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 22: After refmac, R = 0.1808 (Rfree = 0.000) for 1989 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 23: After refmac, R = 0.1745 (Rfree = 0.000) for 1983 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1737 (Rfree = 0.000) for 1979 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1731 (Rfree = 0.000) for 1973 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 0 residues added, 2044 seeds are put forward Round 1: 124 peptides, 24 chains. Longest chain 10 peptides. Score 0.340 Round 2: 143 peptides, 19 chains. Longest chain 16 peptides. Score 0.549 Round 3: 145 peptides, 22 chains. Longest chain 16 peptides. Score 0.496 Round 4: 147 peptides, 21 chains. Longest chain 18 peptides. Score 0.527 Round 5: 137 peptides, 20 chains. Longest chain 13 peptides. Score 0.500 Taking the results from Round 2 Chains 19, Residues 124, Estimated correctness of the model 11.2 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4451 restraints for refining 1993 atoms. 3934 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1847 (Rfree = 0.000) for 1993 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 27: After refmac, R = 0.1733 (Rfree = 0.000) for 1993 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.1726 (Rfree = 0.000) for 1988 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1727 (Rfree = 0.000) for 1985 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1715 (Rfree = 0.000) for 1980 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 0 residues added, 2060 seeds are put forward Round 1: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.344 Round 2: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.467 Round 3: 144 peptides, 22 chains. Longest chain 12 peptides. Score 0.491 Round 4: 151 peptides, 22 chains. Longest chain 14 peptides. Score 0.525 Round 5: 164 peptides, 27 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 4 Chains 22, Residues 129, Estimated correctness of the model 2.3 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4458 restraints for refining 1993 atoms. 3931 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2061 (Rfree = 0.000) for 1993 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 32: After refmac, R = 0.1877 (Rfree = 0.000) for 1989 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.1832 (Rfree = 0.000) for 1980 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1801 (Rfree = 0.000) for 1976 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 1970 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 0 residues added, 2043 seeds are put forward Round 1: 126 peptides, 25 chains. Longest chain 11 peptides. Score 0.327 Round 2: 131 peptides, 24 chains. Longest chain 11 peptides. Score 0.379 Round 3: 126 peptides, 20 chains. Longest chain 13 peptides. Score 0.445 Round 4: 124 peptides, 19 chains. Longest chain 15 peptides. Score 0.457 Round 5: 138 peptides, 21 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4439 restraints for refining 1993 atoms. 3934 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2040 (Rfree = 0.000) for 1993 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.1975 (Rfree = 0.000) for 1985 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.1913 (Rfree = 0.000) for 1976 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1891 (Rfree = 0.000) for 1966 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1865 (Rfree = 0.000) for 1958 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2046 seeds are put forward Round 1: 119 peptides, 21 chains. Longest chain 11 peptides. Score 0.384 Round 2: 132 peptides, 23 chains. Longest chain 15 peptides. Score 0.408 Round 3: 132 peptides, 21 chains. Longest chain 10 peptides. Score 0.453 Round 4: 127 peptides, 20 chains. Longest chain 10 peptides. Score 0.450 Round 5: 121 peptides, 18 chains. Longest chain 11 peptides. Score 0.464 Taking the results from Round 5 Chains 18, Residues 103, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3781 reflections ( 97.05 % complete ) and 4613 restraints for refining 1993 atoms. 4187 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1872 (Rfree = 0.000) for 1993 atoms. Found 7 (15 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.1803 (Rfree = 0.000) for 1990 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1693 (Rfree = 0.000) for 1986 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1674 (Rfree = 0.000) for 1976 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1638 (Rfree = 0.000) for 1972 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward NCS extension: 0 residues added, 2056 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 7 peptides. Score 0.246 Round 2: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.409 Round 3: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.371 Round 4: 105 peptides, 18 chains. Longest chain 9 peptides. Score 0.378 Round 5: 108 peptides, 17 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 91, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2pr7-3_warpNtrace.pdb as input Building loops using Loopy2018 17 chains (91 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3781 reflections ( 97.05 % complete ) and 4727 restraints for refining 1993 atoms. 4365 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1815 (Rfree = 0.000) for 1993 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1721 (Rfree = 0.000) for 1985 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1673 (Rfree = 0.000) for 1978 atoms. Found 0 (14 requested) and removed 2 (7 requested) atoms. Cycle 49: After refmac, R = 0.1618 (Rfree = 0.000) for 1975 atoms. TimeTaking 33.3