Mon 24 Dec 07:30:23 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 2pr7-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-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/2pr7-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-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 07:30:28 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/2pr7-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.2-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 198 and 0 Target number of residues in the AU: 198 Target solvent content: 0.6334 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: 2pr7-3.2-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: 2pr7-3.2-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 3.201 Wilson plot Bfac: 68.14 4512 reflections ( 97.07 % complete ) and 0 restraints for refining 2434 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3160 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2264 (Rfree = 0.000) for 2434 atoms. Found 10 (21 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 2476 seeds are put forward NCS extension: 0 residues added, 2476 seeds are put forward Round 1: 130 peptides, 28 chains. Longest chain 8 peptides. Score 0.277 Round 2: 149 peptides, 25 chains. Longest chain 12 peptides. Score 0.452 Round 3: 156 peptides, 24 chains. Longest chain 13 peptides. Score 0.507 Round 4: 162 peptides, 23 chains. Longest chain 12 peptides. Score 0.554 Round 5: 163 peptides, 22 chains. Longest chain 22 peptides. Score 0.578 Taking the results from Round 5 Chains 23, Residues 141, Estimated correctness of the model 34.9 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 3930 restraints for refining 2001 atoms. 3200 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2479 (Rfree = 0.000) for 2001 atoms. Found 12 (17 requested) and removed 13 (8 requested) atoms. Cycle 2: After refmac, R = 0.2370 (Rfree = 0.000) for 1986 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 3: After refmac, R = 0.2320 (Rfree = 0.000) for 1972 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2393 (Rfree = 0.000) for 1963 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2381 (Rfree = 0.000) for 1957 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 2063 seeds are put forward Round 1: 151 peptides, 25 chains. Longest chain 16 peptides. Score 0.462 Round 2: 160 peptides, 24 chains. Longest chain 13 peptides. Score 0.526 Round 3: 158 peptides, 23 chains. Longest chain 16 peptides. Score 0.537 Round 4: 157 peptides, 22 chains. Longest chain 16 peptides. Score 0.552 Round 5: 156 peptides, 23 chains. Longest chain 18 peptides. Score 0.527 Taking the results from Round 4 Chains 24, Residues 135, Estimated correctness of the model 27.4 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4262 restraints for refining 2001 atoms. 3651 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2457 (Rfree = 0.000) for 2001 atoms. Found 14 (17 requested) and removed 18 (8 requested) atoms. Cycle 7: After refmac, R = 0.2297 (Rfree = 0.000) for 1983 atoms. Found 13 (17 requested) and removed 9 (8 requested) atoms. Cycle 8: After refmac, R = 0.2219 (Rfree = 0.000) for 1980 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.2196 (Rfree = 0.000) for 1973 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2224 (Rfree = 0.000) for 1965 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2054 seeds are put forward Round 1: 140 peptides, 26 chains. Longest chain 9 peptides. Score 0.382 Round 2: 157 peptides, 26 chains. Longest chain 10 peptides. Score 0.470 Round 3: 145 peptides, 20 chains. Longest chain 11 peptides. Score 0.538 Round 4: 152 peptides, 23 chains. Longest chain 12 peptides. Score 0.509 Round 5: 155 peptides, 22 chains. Longest chain 17 peptides. Score 0.543 Taking the results from Round 5 Chains 22, Residues 133, Estimated correctness of the model 24.7 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4274 restraints for refining 2001 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2470 (Rfree = 0.000) for 2001 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 12: After refmac, R = 0.2328 (Rfree = 0.000) for 1997 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 13: After refmac, R = 0.2305 (Rfree = 0.000) for 1992 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2455 (Rfree = 0.000) for 1982 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2314 (Rfree = 0.000) for 1975 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.24 Search for helices and strands: 0 residues in 0 chains, 2015 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2040 seeds are put forward Round 1: 128 peptides, 22 chains. Longest chain 12 peptides. Score 0.409 Round 2: 148 peptides, 19 chains. Longest chain 21 peptides. Score 0.571 Round 3: 145 peptides, 19 chains. Longest chain 20 peptides. Score 0.558 Round 4: 153 peptides, 21 chains. Longest chain 12 peptides. Score 0.554 Round 5: 160 peptides, 22 chains. Longest chain 20 peptides. Score 0.565 Taking the results from Round 2 Chains 21, Residues 129, Estimated correctness of the model 32.9 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4244 restraints for refining 2001 atoms. 3686 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2370 (Rfree = 0.000) for 2001 atoms. Found 6 (17 requested) and removed 14 (8 requested) atoms. Cycle 17: After refmac, R = 0.2142 (Rfree = 0.000) for 1988 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.1986 (Rfree = 0.000) for 1979 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.1922 (Rfree = 0.000) for 1977 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.1856 (Rfree = 0.000) for 1970 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2057 seeds are put forward Round 1: 156 peptides, 28 chains. Longest chain 12 peptides. Score 0.422 Round 2: 148 peptides, 26 chains. Longest chain 10 peptides. Score 0.425 Round 3: 145 peptides, 24 chains. Longest chain 11 peptides. Score 0.453 Round 4: 148 peptides, 23 chains. Longest chain 18 peptides. Score 0.490 Round 5: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 5 Chains 21, Residues 123, Estimated correctness of the model 15.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4436 restraints for refining 2001 atoms. 3965 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2138 (Rfree = 0.000) for 2001 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.1939 (Rfree = 0.000) for 2004 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.1896 (Rfree = 0.000) for 1997 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.1816 (Rfree = 0.000) for 1988 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1780 (Rfree = 0.000) for 1981 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.21 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2077 seeds are put forward Round 1: 130 peptides, 23 chains. Longest chain 11 peptides. Score 0.397 Round 2: 158 peptides, 24 chains. Longest chain 19 peptides. Score 0.517 Round 3: 153 peptides, 25 chains. Longest chain 15 peptides. Score 0.472 Round 4: 156 peptides, 23 chains. Longest chain 15 peptides. Score 0.527 Round 5: 159 peptides, 25 chains. Longest chain 19 peptides. Score 0.501 Taking the results from Round 4 Chains 23, Residues 133, Estimated correctness of the model 19.8 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4372 restraints for refining 2001 atoms. 3852 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2076 (Rfree = 0.000) for 2001 atoms. Found 11 (17 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2125 (Rfree = 0.000) for 2000 atoms. Found 13 (17 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.1971 (Rfree = 0.000) for 1999 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.1780 (Rfree = 0.000) for 1992 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1672 (Rfree = 0.000) for 1987 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.21 Search for helices and strands: 0 residues in 0 chains, 2069 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2086 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 10 peptides. Score 0.332 Round 2: 132 peptides, 22 chains. Longest chain 11 peptides. Score 0.431 Round 3: 135 peptides, 20 chains. Longest chain 12 peptides. Score 0.490 Round 4: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.441 Round 5: 136 peptides, 21 chains. Longest chain 14 peptides. Score 0.474 Taking the results from Round 3 Chains 21, Residues 115, Estimated correctness of the model 8.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4354 restraints for refining 2001 atoms. 3881 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1955 (Rfree = 0.000) for 2001 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.1919 (Rfree = 0.000) for 1997 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.1737 (Rfree = 0.000) for 1993 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.1965 (Rfree = 0.000) for 1981 atoms. Found 8 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1743 (Rfree = 0.000) for 1976 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 2033 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2047 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 9 peptides. Score 0.294 Round 2: 131 peptides, 23 chains. Longest chain 12 peptides. Score 0.402 Round 3: 137 peptides, 23 chains. Longest chain 11 peptides. Score 0.434 Round 4: 143 peptides, 23 chains. Longest chain 12 peptides. Score 0.465 Round 5: 146 peptides, 23 chains. Longest chain 11 peptides. Score 0.480 Taking the results from Round 5 Chains 23, Residues 123, Estimated correctness of the model 4.6 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4315 restraints for refining 2001 atoms. 3807 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2077 (Rfree = 0.000) for 2001 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.2209 (Rfree = 0.000) for 1999 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2266 (Rfree = 0.000) for 1995 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1776 (Rfree = 0.000) for 2000 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1760 (Rfree = 0.000) for 1990 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.322 Round 2: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.376 Round 3: 126 peptides, 19 chains. Longest chain 12 peptides. Score 0.467 Round 4: 133 peptides, 20 chains. Longest chain 14 peptides. Score 0.480 Round 5: 120 peptides, 17 chains. Longest chain 12 peptides. Score 0.482 Taking the results from Round 5 Chains 17, Residues 103, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4512 reflections ( 97.07 % complete ) and 4537 restraints for refining 2001 atoms. 4142 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1944 (Rfree = 0.000) for 2001 atoms. Found 13 (17 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1767 (Rfree = 0.000) for 2006 atoms. Found 10 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1708 (Rfree = 0.000) for 2007 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1803 (Rfree = 0.000) for 2002 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2041 (Rfree = 0.000) for 1995 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2057 seeds are put forward NCS extension: 0 residues added, 2057 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 9 peptides. Score 0.283 Round 2: 121 peptides, 20 chains. Longest chain 12 peptides. Score 0.418 Round 3: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.416 Round 4: 118 peptides, 20 chains. Longest chain 13 peptides. Score 0.402 Round 5: 126 peptides, 21 chains. Longest chain 12 peptides. Score 0.422 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 105, 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. 4512 reflections ( 97.07 % complete ) and 4529 restraints for refining 2001 atoms. 4130 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1980 (Rfree = 0.000) for 2001 atoms. Found 0 (17 requested) and removed 6 (8 requested) atoms. Cycle 47: After refmac, R = 0.1927 (Rfree = 0.000) for 1994 atoms. Found 0 (17 requested) and removed 2 (8 requested) atoms. Cycle 48: After refmac, R = 0.1910 (Rfree = 0.000) for 1992 atoms. Found 0 (17 requested) and removed 3 (8 requested) atoms. Cycle 49: After refmac, R = 0.1804 (Rfree = 0.000) for 1987 atoms. Found 0 (17 requested) and removed 4 (8 requested) atoms. Writing output files ... TimeTaking 25.75