Sun 23 Dec 22:23:05 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 2pr7-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-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/2pr7-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-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 22:23:13 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/2pr7-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-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 181 and 0 Target number of residues in the AU: 181 Target solvent content: 0.6649 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: 2pr7-4.0-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: 2pr7-4.0-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 4.001 Wilson plot Bfac: 87.27 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2313 reflections ( 96.70 % complete ) and 0 restraints for refining 2413 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3213 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2964 (Rfree = 0.000) for 2413 atoms. Found 11 (11 requested) and removed 31 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 2437 seeds are put forward NCS extension: 0 residues added, 2437 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 6 peptides. Score 0.228 Round 2: 113 peptides, 21 chains. Longest chain 10 peptides. Score 0.349 Round 3: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.335 Round 4: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.417 Round 5: 115 peptides, 18 chains. Longest chain 11 peptides. Score 0.433 Taking the results from Round 5 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4806 restraints for refining 1978 atoms. 4421 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2235 (Rfree = 0.000) for 1978 atoms. Found 4 (9 requested) and removed 19 (4 requested) atoms. Cycle 2: After refmac, R = 0.2137 (Rfree = 0.000) for 1928 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 3: After refmac, R = 0.1951 (Rfree = 0.000) for 1904 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.1774 (Rfree = 0.000) for 1895 atoms. Found 5 (9 requested) and removed 12 (4 requested) atoms. Cycle 5: After refmac, R = 0.1562 (Rfree = 0.000) for 1882 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 1942 seeds are put forward NCS extension: 0 residues added, 1942 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 6 peptides. Score 0.239 Round 2: 127 peptides, 21 chains. Longest chain 13 peptides. Score 0.427 Round 3: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.438 Round 4: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.442 Round 5: 127 peptides, 19 chains. Longest chain 13 peptides. Score 0.473 Taking the results from Round 5 Chains 19, Residues 108, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4210 restraints for refining 1901 atoms. 3756 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2069 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 7: After refmac, R = 0.1712 (Rfree = 0.000) for 1881 atoms. Found 7 (8 requested) and removed 15 (4 requested) atoms. Cycle 8: After refmac, R = 0.1737 (Rfree = 0.000) for 1865 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.1348 (Rfree = 0.000) for 1858 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.1727 (Rfree = 0.000) for 1852 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 1936 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1949 seeds are put forward Round 1: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.385 Round 2: 107 peptides, 17 chains. Longest chain 10 peptides. Score 0.414 Round 3: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.414 Round 4: 113 peptides, 16 chains. Longest chain 13 peptides. Score 0.469 Round 5: 113 peptides, 16 chains. Longest chain 13 peptides. Score 0.469 Taking the results from Round 5 Chains 17, Residues 97, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4535 restraints for refining 1979 atoms. 4106 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1883 (Rfree = 0.000) for 1979 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 12: After refmac, R = 0.1640 (Rfree = 0.000) for 1956 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.1533 (Rfree = 0.000) for 1943 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.1467 (Rfree = 0.000) for 1937 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.1538 (Rfree = 0.000) for 1926 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 2000 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2013 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.279 Round 2: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.398 Round 3: 120 peptides, 22 chains. Longest chain 12 peptides. Score 0.365 Round 4: 106 peptides, 17 chains. Longest chain 12 peptides. Score 0.408 Round 5: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 4 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4697 restraints for refining 1951 atoms. 4358 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1803 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 17: After refmac, R = 0.1819 (Rfree = 0.000) for 1933 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 18: After refmac, R = 0.1594 (Rfree = 0.000) for 1928 atoms. Found 8 (9 requested) and removed 13 (4 requested) atoms. Cycle 19: After refmac, R = 0.1410 (Rfree = 0.000) for 1920 atoms. Found 2 (9 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.1348 (Rfree = 0.000) for 1908 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 1975 seeds are put forward NCS extension: 0 residues added, 1975 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 6 peptides. Score 0.240 Round 2: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.395 Round 3: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.435 Round 4: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.411 Round 5: 119 peptides, 19 chains. Longest chain 12 peptides. Score 0.431 Taking the results from Round 3 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4535 restraints for refining 1965 atoms. 4134 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1562 (Rfree = 0.000) for 1965 atoms. Found 8 (9 requested) and removed 14 (4 requested) atoms. Cycle 22: After refmac, R = 0.1560 (Rfree = 0.000) for 1946 atoms. Found 7 (9 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.1427 (Rfree = 0.000) for 1936 atoms. Found 2 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.1283 (Rfree = 0.000) for 1927 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.1428 (Rfree = 0.000) for 1922 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 1983 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1998 seeds are put forward Round 1: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.317 Round 2: 123 peptides, 22 chains. Longest chain 12 peptides. Score 0.382 Round 3: 122 peptides, 20 chains. Longest chain 13 peptides. Score 0.424 Round 4: 129 peptides, 18 chains. Longest chain 24 peptides. Score 0.504 Round 5: 122 peptides, 18 chains. Longest chain 26 peptides. Score 0.470 Taking the results from Round 4 Chains 20, Residues 111, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4441 restraints for refining 1970 atoms. 3969 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1731 (Rfree = 0.000) for 1970 atoms. Found 3 (9 requested) and removed 14 (4 requested) atoms. Cycle 27: After refmac, R = 0.1582 (Rfree = 0.000) for 1953 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.1462 (Rfree = 0.000) for 1943 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.1601 (Rfree = 0.000) for 1936 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.1247 (Rfree = 0.000) for 1933 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 1998 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2022 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.323 Round 2: 120 peptides, 19 chains. Longest chain 11 peptides. Score 0.436 Round 3: 114 peptides, 15 chains. Longest chain 13 peptides. Score 0.497 Round 4: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.446 Round 5: 108 peptides, 16 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 3 Chains 15, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4596 restraints for refining 1973 atoms. 4215 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1522 (Rfree = 0.000) for 1973 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.1536 (Rfree = 0.000) for 1962 atoms. Found 3 (9 requested) and removed 9 (4 requested) atoms. Cycle 33: After refmac, R = 0.1497 (Rfree = 0.000) for 1951 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.1484 (Rfree = 0.000) for 1941 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1550 (Rfree = 0.000) for 1938 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2015 seeds are put forward Round 1: 108 peptides, 20 chains. Longest chain 8 peptides. Score 0.345 Round 2: 124 peptides, 23 chains. Longest chain 12 peptides. Score 0.364 Round 3: 125 peptides, 20 chains. Longest chain 18 peptides. Score 0.440 Round 4: 132 peptides, 21 chains. Longest chain 13 peptides. Score 0.453 Round 5: 125 peptides, 20 chains. Longest chain 11 peptides. Score 0.440 Taking the results from Round 4 Chains 21, Residues 111, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4377 restraints for refining 1952 atoms. 3945 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1911 (Rfree = 0.000) for 1952 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 37: After refmac, R = 0.1650 (Rfree = 0.000) for 1940 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.1396 (Rfree = 0.000) for 1929 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1799 (Rfree = 0.000) for 1924 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1471 (Rfree = 0.000) for 1923 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.77 Search for helices and strands: 0 residues in 0 chains, 1982 seeds are put forward NCS extension: 0 residues added, 1982 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 8 peptides. Score 0.257 Round 2: 88 peptides, 15 chains. Longest chain 10 peptides. Score 0.355 Round 3: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.355 Round 4: 92 peptides, 15 chains. Longest chain 10 peptides. Score 0.379 Round 5: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 5 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4476 restraints for refining 1980 atoms. 4104 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1984 (Rfree = 0.000) for 1980 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 42: After refmac, R = 0.1596 (Rfree = 0.000) for 1968 atoms. Found 5 (9 requested) and removed 13 (4 requested) atoms. Cycle 43: After refmac, R = 0.1339 (Rfree = 0.000) for 1957 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.1509 (Rfree = 0.000) for 1952 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1284 (Rfree = 0.000) for 1951 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.77 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward NCS extension: 0 residues added, 2019 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 8 peptides. Score 0.248 Round 2: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.300 Round 3: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.302 Round 4: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.341 Round 5: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, 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 2pr7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2313 reflections ( 96.70 % complete ) and 4806 restraints for refining 1980 atoms. 4526 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1433 (Rfree = 0.000) for 1980 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1309 (Rfree = 0.000) for 1969 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1332 (Rfree = 0.000) for 1962 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1210 (Rfree = 0.000) for 1955 atoms. TimeTaking 31.67