Mon 24 Dec 00:44:33 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gnr-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-4.0-parrot-mrncs ############### 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 00:44:37 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-4.0-parrot-mrncs/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 196 and 0 Target number of residues in the AU: 196 Target solvent content: 0.6745 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.52 Input MTZ file: 2gnr-4.0-parrot-mrncs.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: 91 Cell parameters: 75.160 75.160 115.370 90.000 90.000 90.000 Input sequence file: 2gnr-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.70 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: 75.160 4.000 Wilson plot Bfac: 95.39 3072 reflections ( 99.19 % complete ) and 0 restraints for refining 2561 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3520 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3423 (Rfree = 0.000) for 2561 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.91 3.81 Search for helices and strands: 0 residues in 0 chains, 2590 seeds are put forward NCS extension: 0 residues added, 2590 seeds are put forward Round 1: 106 peptides, 20 chains. Longest chain 11 peptides. Score 0.321 Round 2: 119 peptides, 18 chains. Longest chain 14 peptides. Score 0.433 Round 3: 135 peptides, 20 chains. Longest chain 13 peptides. Score 0.466 Round 4: 145 peptides, 18 chains. Longest chain 17 peptides. Score 0.549 Round 5: 150 peptides, 21 chains. Longest chain 16 peptides. Score 0.513 Taking the results from Round 4 Chains 18, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4986 restraints for refining 2093 atoms. 4496 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2736 (Rfree = 0.000) for 2093 atoms. Found 2 (9 requested) and removed 19 (4 requested) atoms. Cycle 2: After refmac, R = 0.2432 (Rfree = 0.000) for 2047 atoms. Found 2 (9 requested) and removed 13 (4 requested) atoms. Cycle 3: After refmac, R = 0.2239 (Rfree = 0.000) for 2019 atoms. Found 1 (9 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2387 (Rfree = 0.000) for 1996 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 5: After refmac, R = 0.2240 (Rfree = 0.000) for 1982 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2058 seeds are put forward Round 1: 129 peptides, 21 chains. Longest chain 21 peptides. Score 0.417 Round 2: 144 peptides, 21 chains. Longest chain 13 peptides. Score 0.487 Round 3: 149 peptides, 20 chains. Longest chain 18 peptides. Score 0.528 Round 4: 157 peptides, 19 chains. Longest chain 23 peptides. Score 0.579 Round 5: 152 peptides, 20 chains. Longest chain 16 peptides. Score 0.541 Taking the results from Round 4 Chains 19, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4931 restraints for refining 2095 atoms. 4398 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2695 (Rfree = 0.000) for 2095 atoms. Found 6 (9 requested) and removed 28 (4 requested) atoms. Cycle 7: After refmac, R = 0.2482 (Rfree = 0.000) for 2055 atoms. Found 6 (9 requested) and removed 17 (4 requested) atoms. Cycle 8: After refmac, R = 0.2499 (Rfree = 0.000) for 2033 atoms. Found 5 (9 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.2475 (Rfree = 0.000) for 2009 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 10: After refmac, R = 0.2484 (Rfree = 0.000) for 1989 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2078 seeds are put forward Round 1: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.339 Round 2: 128 peptides, 20 chains. Longest chain 12 peptides. Score 0.434 Round 3: 129 peptides, 22 chains. Longest chain 12 peptides. Score 0.396 Round 4: 137 peptides, 19 chains. Longest chain 14 peptides. Score 0.496 Round 5: 134 peptides, 17 chains. Longest chain 14 peptides. Score 0.522 Taking the results from Round 5 Chains 17, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4917 restraints for refining 2095 atoms. 4466 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2278 (Rfree = 0.000) for 2095 atoms. Found 3 (9 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.2362 (Rfree = 0.000) for 2060 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 13: After refmac, R = 0.2236 (Rfree = 0.000) for 2032 atoms. Found 8 (9 requested) and removed 16 (4 requested) atoms. Cycle 14: After refmac, R = 0.2396 (Rfree = 0.000) for 2010 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 15: After refmac, R = 0.2139 (Rfree = 0.000) for 1998 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 2076 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2090 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 8 peptides. Score 0.286 Round 2: 122 peptides, 18 chains. Longest chain 13 peptides. Score 0.447 Round 3: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.401 Round 4: 119 peptides, 16 chains. Longest chain 21 peptides. Score 0.476 Round 5: 123 peptides, 17 chains. Longest chain 14 peptides. Score 0.473 Taking the results from Round 4 Chains 16, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4782 restraints for refining 2071 atoms. 4386 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2072 (Rfree = 0.000) for 2071 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 17: After refmac, R = 0.2069 (Rfree = 0.000) for 2044 atoms. Found 6 (9 requested) and removed 15 (4 requested) atoms. Cycle 18: After refmac, R = 0.2075 (Rfree = 0.000) for 2023 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 19: After refmac, R = 0.2224 (Rfree = 0.000) for 2011 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.2165 (Rfree = 0.000) for 1999 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 2075 seeds are put forward NCS extension: 0 residues added, 2075 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 9 peptides. Score 0.299 Round 2: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.362 Round 3: 130 peptides, 20 chains. Longest chain 14 peptides. Score 0.443 Round 4: 130 peptides, 21 chains. Longest chain 13 peptides. Score 0.422 Round 5: 137 peptides, 22 chains. Longest chain 19 peptides. Score 0.435 Taking the results from Round 3 Chains 20, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4513 restraints for refining 2011 atoms. 4093 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1928 (Rfree = 0.000) for 2011 atoms. Found 4 (9 requested) and removed 14 (4 requested) atoms. Cycle 22: After refmac, R = 0.2053 (Rfree = 0.000) for 1981 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2318 (Rfree = 0.000) for 1966 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.2131 (Rfree = 0.000) for 1953 atoms. Found 3 (9 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.2202 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 1999 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2012 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 13 peptides. Score 0.281 Round 2: 125 peptides, 21 chains. Longest chain 17 peptides. Score 0.397 Round 3: 131 peptides, 22 chains. Longest chain 21 peptides. Score 0.406 Round 4: 134 peptides, 22 chains. Longest chain 16 peptides. Score 0.420 Round 5: 126 peptides, 19 chains. Longest chain 23 peptides. Score 0.445 Taking the results from Round 5 Chains 19, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4618 restraints for refining 2038 atoms. 4209 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 2038 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.2181 (Rfree = 0.000) for 2025 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 28: After refmac, R = 0.2452 (Rfree = 0.000) for 2007 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 29: After refmac, R = 0.2755 (Rfree = 0.000) for 1992 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.2350 (Rfree = 0.000) for 1973 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 2046 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2074 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 6 peptides. Score 0.239 Round 2: 123 peptides, 23 chains. Longest chain 12 peptides. Score 0.343 Round 3: 119 peptides, 21 chains. Longest chain 12 peptides. Score 0.367 Round 4: 119 peptides, 18 chains. Longest chain 21 peptides. Score 0.433 Round 5: 123 peptides, 19 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 4 Chains 19, Residues 101, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4598 restraints for refining 2075 atoms. 4171 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2459 (Rfree = 0.000) for 2075 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 32: After refmac, R = 0.2464 (Rfree = 0.000) for 2050 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 33: After refmac, R = 0.2103 (Rfree = 0.000) for 2032 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 34: After refmac, R = 0.2292 (Rfree = 0.000) for 2017 atoms. Found 4 (9 requested) and removed 16 (4 requested) atoms. Cycle 35: After refmac, R = 0.1958 (Rfree = 0.000) for 1993 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2076 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 7 peptides. Score 0.219 Round 2: 110 peptides, 21 chains. Longest chain 9 peptides. Score 0.319 Round 3: 109 peptides, 17 chains. Longest chain 10 peptides. Score 0.405 Round 4: 109 peptides, 17 chains. Longest chain 11 peptides. Score 0.405 Round 5: 95 peptides, 15 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 4 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4865 restraints for refining 2092 atoms. 4514 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2382 (Rfree = 0.000) for 2092 atoms. Found 9 (9 requested) and removed 78 (4 requested) atoms. Cycle 37: After refmac, R = 0.1954 (Rfree = 0.000) for 2016 atoms. Found 3 (9 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.1906 (Rfree = 0.000) for 2001 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 39: After refmac, R = 0.1970 (Rfree = 0.000) for 1991 atoms. Found 1 (9 requested) and removed 18 (4 requested) atoms. Cycle 40: After refmac, R = 0.1931 (Rfree = 0.000) for 1971 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 3.76 Search for helices and strands: 0 residues in 0 chains, 2018 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2032 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 8 peptides. Score 0.213 Round 2: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.279 Round 3: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.286 Round 4: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.335 Round 5: 99 peptides, 18 chains. Longest chain 10 peptides. Score 0.330 Taking the results from Round 4 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3072 reflections ( 99.19 % complete ) and 4775 restraints for refining 2028 atoms. 4465 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2047 (Rfree = 0.000) for 2028 atoms. Found 2 (9 requested) and removed 29 (4 requested) atoms. Cycle 42: After refmac, R = 0.2102 (Rfree = 0.000) for 1993 atoms. Found 8 (9 requested) and removed 16 (4 requested) atoms. Cycle 43: After refmac, R = 0.1937 (Rfree = 0.000) for 1981 atoms. Found 5 (9 requested) and removed 24 (4 requested) atoms. Cycle 44: After refmac, R = 0.1782 (Rfree = 0.000) for 1955 atoms. Found 1 (9 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.1751 (Rfree = 0.000) for 1944 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.94 3.84 Search for helices and strands: 0 residues in 0 chains, 1980 seeds are put forward NCS extension: 0 residues added, 1980 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 9 peptides. Score 0.211 Round 2: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.270 Round 3: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.279 Round 4: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.296 Round 5: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.267 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 75, 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 2gnr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3072 reflections ( 99.19 % complete ) and 4680 restraints for refining 2001 atoms. 4398 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2533 (Rfree = 0.000) for 2001 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2184 (Rfree = 0.000) for 1987 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2256 (Rfree = 0.000) for 1978 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2380 (Rfree = 0.000) for 1972 atoms. TimeTaking 26.42