Mon 24 Dec 07:35:56 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 2pr7-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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/2pr7-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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 07:36:00 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/2pr7-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.6-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 193 and 0 Target number of residues in the AU: 193 Target solvent content: 0.6427 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: 2pr7-3.6-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: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-3.6-parrot-noncs.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 3.600 Wilson plot Bfac: 72.71 3180 reflections ( 96.95 % complete ) and 0 restraints for refining 2421 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3214 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2709 (Rfree = 0.000) for 2421 atoms. Found 15 (15 requested) and removed 39 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 2448 seeds are put forward NCS extension: 0 residues added, 2448 seeds are put forward Round 1: 113 peptides, 24 chains. Longest chain 7 peptides. Score 0.275 Round 2: 140 peptides, 23 chains. Longest chain 16 peptides. Score 0.450 Round 3: 146 peptides, 23 chains. Longest chain 11 peptides. Score 0.480 Round 4: 140 peptides, 21 chains. Longest chain 18 peptides. Score 0.493 Round 5: 135 peptides, 21 chains. Longest chain 18 peptides. Score 0.469 Taking the results from Round 4 Chains 21, Residues 119, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4540 restraints for refining 1987 atoms. 4067 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2056 (Rfree = 0.000) for 1987 atoms. Found 11 (12 requested) and removed 17 (6 requested) atoms. Cycle 2: After refmac, R = 0.1845 (Rfree = 0.000) for 1951 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. Cycle 3: After refmac, R = 0.1755 (Rfree = 0.000) for 1935 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.1630 (Rfree = 0.000) for 1928 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.1640 (Rfree = 0.000) for 1922 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2024 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 8 peptides. Score 0.269 Round 2: 125 peptides, 18 chains. Longest chain 11 peptides. Score 0.485 Round 3: 127 peptides, 18 chains. Longest chain 11 peptides. Score 0.495 Round 4: 127 peptides, 20 chains. Longest chain 10 peptides. Score 0.450 Round 5: 127 peptides, 16 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 5 Chains 16, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4665 restraints for refining 1965 atoms. 4237 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2086 (Rfree = 0.000) for 1965 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.1923 (Rfree = 0.000) for 1948 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.1872 (Rfree = 0.000) for 1941 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2178 (Rfree = 0.000) for 1939 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 10: After refmac, R = 0.1765 (Rfree = 0.000) for 1933 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 2021 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2035 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.325 Round 2: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.395 Round 3: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Round 4: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.442 Round 5: 115 peptides, 18 chains. Longest chain 11 peptides. Score 0.433 Taking the results from Round 4 Chains 19, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4643 restraints for refining 1987 atoms. 4254 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1879 (Rfree = 0.000) for 1987 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 12: After refmac, R = 0.1833 (Rfree = 0.000) for 1964 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.1754 (Rfree = 0.000) for 1964 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.1722 (Rfree = 0.000) for 1960 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.1776 (Rfree = 0.000) for 1949 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2009 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2025 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.313 Round 2: 132 peptides, 21 chains. Longest chain 21 peptides. Score 0.453 Round 3: 125 peptides, 20 chains. Longest chain 19 peptides. Score 0.440 Round 4: 130 peptides, 21 chains. Longest chain 11 peptides. Score 0.443 Round 5: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.418 Taking the results from Round 2 Chains 21, Residues 111, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4434 restraints for refining 1986 atoms. 3963 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1809 (Rfree = 0.000) for 1986 atoms. Found 11 (12 requested) and removed 17 (6 requested) atoms. Cycle 17: After refmac, R = 0.1615 (Rfree = 0.000) for 1969 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1552 (Rfree = 0.000) for 1958 atoms. Found 2 (12 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.1488 (Rfree = 0.000) for 1947 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.1519 (Rfree = 0.000) for 1936 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 2001 seeds are put forward NCS extension: 40 residues added (7 deleted due to clashes), 2041 seeds are put forward Round 1: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.381 Round 2: 121 peptides, 20 chains. Longest chain 11 peptides. Score 0.418 Round 3: 127 peptides, 17 chains. Longest chain 14 peptides. Score 0.516 Round 4: 133 peptides, 19 chains. Longest chain 12 peptides. Score 0.502 Round 5: 133 peptides, 18 chains. Longest chain 12 peptides. Score 0.524 Taking the results from Round 5 Chains 18, Residues 115, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4462 restraints for refining 1986 atoms. 3992 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1859 (Rfree = 0.000) for 1986 atoms. Found 10 (12 requested) and removed 19 (6 requested) atoms. Cycle 22: After refmac, R = 0.1638 (Rfree = 0.000) for 1971 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.1571 (Rfree = 0.000) for 1965 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.1511 (Rfree = 0.000) for 1957 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.1506 (Rfree = 0.000) for 1948 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2009 seeds are put forward Round 1: 91 peptides, 17 chains. Longest chain 11 peptides. Score 0.320 Round 2: 107 peptides, 18 chains. Longest chain 11 peptides. Score 0.389 Round 3: 114 peptides, 18 chains. Longest chain 14 peptides. Score 0.428 Round 4: 113 peptides, 19 chains. Longest chain 9 peptides. Score 0.398 Round 5: 119 peptides, 19 chains. Longest chain 11 peptides. Score 0.431 Taking the results from Round 5 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4536 restraints for refining 1986 atoms. 4121 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1753 (Rfree = 0.000) for 1986 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 27: After refmac, R = 0.1718 (Rfree = 0.000) for 1979 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.1764 (Rfree = 0.000) for 1976 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.1620 (Rfree = 0.000) for 1975 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.1650 (Rfree = 0.000) for 1975 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2049 seeds are put forward NCS extension: 0 residues added, 2049 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 10 peptides. Score 0.299 Round 2: 116 peptides, 23 chains. Longest chain 9 peptides. Score 0.318 Round 3: 120 peptides, 22 chains. Longest chain 8 peptides. Score 0.365 Round 4: 122 peptides, 22 chains. Longest chain 10 peptides. Score 0.376 Round 5: 125 peptides, 23 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 4 Chains 22, Residues 100, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4563 restraints for refining 1987 atoms. 4140 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1771 (Rfree = 0.000) for 1987 atoms. Found 6 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.1684 (Rfree = 0.000) for 1971 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.1674 (Rfree = 0.000) for 1962 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.1598 (Rfree = 0.000) for 1964 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.1582 (Rfree = 0.000) for 1957 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2030 seeds are put forward NCS extension: 0 residues added, 2030 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.305 Round 2: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.311 Round 3: 95 peptides, 15 chains. Longest chain 10 peptides. Score 0.396 Round 4: 104 peptides, 17 chains. Longest chain 8 peptides. Score 0.397 Round 5: 108 peptides, 18 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4827 restraints for refining 1987 atoms. 4496 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1676 (Rfree = 0.000) for 1987 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 37: After refmac, R = 0.1698 (Rfree = 0.000) for 1981 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.1468 (Rfree = 0.000) for 1979 atoms. Found 10 (12 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.1777 (Rfree = 0.000) for 1974 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.1443 (Rfree = 0.000) for 1973 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 0 residues added, 2048 seeds are put forward Round 1: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.295 Round 2: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.363 Round 3: 117 peptides, 19 chains. Longest chain 13 peptides. Score 0.420 Round 4: 126 peptides, 21 chains. Longest chain 10 peptides. Score 0.422 Round 5: 128 peptides, 22 chains. Longest chain 9 peptides. Score 0.409 Taking the results from Round 4 Chains 21, Residues 105, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3180 reflections ( 96.95 % complete ) and 4578 restraints for refining 1987 atoms. 4160 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1650 (Rfree = 0.000) for 1987 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.1708 (Rfree = 0.000) for 1980 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1495 (Rfree = 0.000) for 1984 atoms. Found 7 (12 requested) and removed 11 (6 requested) atoms. Cycle 44: After refmac, R = 0.1730 (Rfree = 0.000) for 1979 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1443 (Rfree = 0.000) for 1980 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 2058 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2064 seeds are put forward Round 1: 96 peptides, 22 chains. Longest chain 6 peptides. Score 0.220 Round 2: 123 peptides, 23 chains. Longest chain 10 peptides. Score 0.358 Round 3: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.374 Round 4: 111 peptides, 20 chains. Longest chain 9 peptides. Score 0.363 Round 5: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.362 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 93, 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 2pr7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3180 reflections ( 96.95 % complete ) and 4654 restraints for refining 1987 atoms. 4302 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1726 (Rfree = 0.000) for 1987 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1748 (Rfree = 0.000) for 1979 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1700 (Rfree = 0.000) for 1973 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1587 (Rfree = 0.000) for 1962 atoms. TimeTaking 26.28