null Mon 24 Dec 07:40:25 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 2hq7-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.8-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/2hq7-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.8-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 07:40:29 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/2hq7-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.8-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 184 and 0 Target number of residues in the AU: 184 Target solvent content: 0.6484 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-3.8-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.80 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: 89.671 3.800 Wilson plot Bfac: 76.26 2895 reflections ( 99.18 % complete ) and 0 restraints for refining 2592 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3347 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3291 (Rfree = 0.000) for 2592 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 2630 seeds are put forward NCS extension: 0 residues added, 2630 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.310 Round 2: 115 peptides, 20 chains. Longest chain 16 peptides. Score 0.391 Round 3: 146 peptides, 21 chains. Longest chain 18 peptides. Score 0.530 Round 4: 159 peptides, 20 chains. Longest chain 25 peptides. Score 0.608 Round 5: 145 peptides, 21 chains. Longest chain 16 peptides. Score 0.526 Taking the results from Round 4 Chains 20, Residues 139, Estimated correctness of the model 2.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4807 restraints for refining 2112 atoms. 4271 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2757 (Rfree = 0.000) for 2112 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.2436 (Rfree = 0.000) for 2066 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 3: After refmac, R = 0.2450 (Rfree = 0.000) for 2040 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 4: After refmac, R = 0.2479 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 5: After refmac, R = 0.2533 (Rfree = 0.000) for 2018 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.81 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 45 residues added (1 deleted due to clashes), 2168 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 10 peptides. Score 0.302 Round 2: 137 peptides, 24 chains. Longest chain 13 peptides. Score 0.418 Round 3: 144 peptides, 23 chains. Longest chain 11 peptides. Score 0.478 Round 4: 149 peptides, 24 chains. Longest chain 19 peptides. Score 0.481 Round 5: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.479 Taking the results from Round 4 Chains 24, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4626 restraints for refining 2010 atoms. 4150 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2434 (Rfree = 0.000) for 2010 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.2324 (Rfree = 0.000) for 1983 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 8: After refmac, R = 0.2170 (Rfree = 0.000) for 1964 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.2224 (Rfree = 0.000) for 1951 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 10: After refmac, R = 0.2154 (Rfree = 0.000) for 1944 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.89 Search for helices and strands: 0 residues in 0 chains, 2039 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 2056 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.285 Round 2: 138 peptides, 24 chains. Longest chain 12 peptides. Score 0.423 Round 3: 143 peptides, 23 chains. Longest chain 12 peptides. Score 0.472 Round 4: 143 peptides, 21 chains. Longest chain 12 peptides. Score 0.516 Round 5: 150 peptides, 19 chains. Longest chain 16 peptides. Score 0.589 Taking the results from Round 5 Chains 19, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4604 restraints for refining 2027 atoms. 4099 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2108 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 12: After refmac, R = 0.1929 (Rfree = 0.000) for 1994 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.2125 (Rfree = 0.000) for 1983 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 14: After refmac, R = 0.1989 (Rfree = 0.000) for 1972 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.2064 (Rfree = 0.000) for 1961 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.81 Search for helices and strands: 0 residues in 0 chains, 2037 seeds are put forward NCS extension: 0 residues added, 2037 seeds are put forward Round 1: 125 peptides, 26 chains. Longest chain 10 peptides. Score 0.300 Round 2: 132 peptides, 22 chains. Longest chain 11 peptides. Score 0.437 Round 3: 139 peptides, 23 chains. Longest chain 12 peptides. Score 0.452 Round 4: 142 peptides, 22 chains. Longest chain 12 peptides. Score 0.489 Round 5: 135 peptides, 21 chains. Longest chain 12 peptides. Score 0.476 Taking the results from Round 4 Chains 22, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4689 restraints for refining 2052 atoms. 4231 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2068 (Rfree = 0.000) for 2052 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2034 (Rfree = 0.000) for 2038 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.1885 (Rfree = 0.000) for 2034 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 19: After refmac, R = 0.2071 (Rfree = 0.000) for 2030 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.1937 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 2124 seeds are put forward NCS extension: 0 residues added, 2124 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 7 peptides. Score 0.279 Round 2: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.383 Round 3: 114 peptides, 20 chains. Longest chain 20 peptides. Score 0.385 Round 4: 110 peptides, 18 chains. Longest chain 16 peptides. Score 0.412 Round 5: 116 peptides, 20 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 4 Chains 18, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 5003 restraints for refining 2113 atoms. 4653 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2043 (Rfree = 0.000) for 2113 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 22: After refmac, R = 0.2230 (Rfree = 0.000) for 2096 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.1948 (Rfree = 0.000) for 2089 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2009 (Rfree = 0.000) for 2083 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1901 (Rfree = 0.000) for 2084 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward NCS extension: 0 residues added, 2144 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.236 Round 2: 119 peptides, 24 chains. Longest chain 9 peptides. Score 0.314 Round 3: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.359 Round 4: 114 peptides, 20 chains. Longest chain 9 peptides. Score 0.385 Round 5: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.373 Taking the results from Round 4 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 5092 restraints for refining 2113 atoms. 4736 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1884 (Rfree = 0.000) for 2113 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2082 (Rfree = 0.000) for 2095 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2029 (Rfree = 0.000) for 2085 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2008 (Rfree = 0.000) for 2077 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.2027 (Rfree = 0.000) for 2072 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 2154 seeds are put forward NCS extension: 0 residues added, 2154 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.258 Round 2: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.337 Round 3: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.389 Round 4: 102 peptides, 21 chains. Longest chain 9 peptides. Score 0.287 Round 5: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.341 Taking the results from Round 3 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4836 restraints for refining 2055 atoms. 4502 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1964 (Rfree = 0.000) for 2055 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 32: After refmac, R = 0.2018 (Rfree = 0.000) for 2041 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.1893 (Rfree = 0.000) for 2032 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.1803 (Rfree = 0.000) for 2029 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 35: After refmac, R = 0.1375 (Rfree = 0.000) for 2027 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 2094 seeds are put forward NCS extension: 0 residues added, 2094 seeds are put forward Round 1: 84 peptides, 19 chains. Longest chain 7 peptides. Score 0.223 Round 2: 92 peptides, 18 chains. Longest chain 10 peptides. Score 0.304 Round 3: 105 peptides, 20 chains. Longest chain 12 peptides. Score 0.332 Round 4: 91 peptides, 13 chains. Longest chain 14 peptides. Score 0.430 Round 5: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 4 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4948 restraints for refining 2045 atoms. 4649 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2027 (Rfree = 0.000) for 2045 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.2234 (Rfree = 0.000) for 2044 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2144 (Rfree = 0.000) for 2040 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2318 (Rfree = 0.000) for 2035 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.2101 (Rfree = 0.000) for 2033 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2120 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 5 peptides. Score 0.209 Round 2: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.346 Round 3: 80 peptides, 14 chains. Longest chain 8 peptides. Score 0.337 Round 4: 70 peptides, 11 chains. Longest chain 9 peptides. Score 0.359 Round 5: 70 peptides, 11 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 5 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2895 reflections ( 99.18 % complete ) and 4651 restraints for refining 1958 atoms. 4426 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2128 (Rfree = 0.000) for 1958 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 42: After refmac, R = 0.2252 (Rfree = 0.000) for 1952 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 43: After refmac, R = 0.1444 (Rfree = 0.000) for 1949 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1252 (Rfree = 0.000) for 1943 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1278 (Rfree = 0.000) for 1938 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 1999 seeds are put forward NCS extension: 0 residues added, 1999 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 8 peptides. Score 0.250 Round 2: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.329 Round 3: 93 peptides, 18 chains. Longest chain 10 peptides. Score 0.310 Round 4: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.322 Round 5: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 88, 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 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2895 reflections ( 99.18 % complete ) and 4688 restraints for refining 1975 atoms. 4355 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1981 (Rfree = 0.000) for 1975 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2253 (Rfree = 0.000) for 1964 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2011 (Rfree = 0.000) for 1952 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2000 (Rfree = 0.000) for 1941 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:09:04 GMT 2018 Job finished. TimeTaking 28.65 Used memory is bytes: 3427856