Sun 23 Dec 22:23:01 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 2inb-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-3.8-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/2inb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-3.8-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 22:23:11 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/2inb-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-3.8-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 95 and 0 Target number of residues in the AU: 95 Target solvent content: 0.6486 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.48 Input MTZ file: 2inb-3.8-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: 152 Cell parameters: 59.524 59.524 71.521 90.000 90.000 120.000 Input sequence file: 2inb-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.762 3.800 Wilson plot Bfac: 76.85 1593 reflections ( 99.75 % complete ) and 0 restraints for refining 1246 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3553 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3249 (Rfree = 0.000) for 1246 atoms. Found 5 (6 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 1264 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.219 Round 2: 68 peptides, 11 chains. Longest chain 18 peptides. Score 0.452 Round 3: 70 peptides, 10 chains. Longest chain 13 peptides. Score 0.515 Round 4: 73 peptides, 9 chains. Longest chain 26 peptides. Score 0.582 Round 5: 70 peptides, 10 chains. Longest chain 12 peptides. Score 0.515 Taking the results from Round 4 Chains 9, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2356 restraints for refining 1009 atoms. 2109 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2709 (Rfree = 0.000) for 1009 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 2: After refmac, R = 0.2240 (Rfree = 0.000) for 985 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 3: After refmac, R = 0.2151 (Rfree = 0.000) for 976 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 4: After refmac, R = 0.2422 (Rfree = 0.000) for 970 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. Cycle 5: After refmac, R = 0.2113 (Rfree = 0.000) for 961 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 995 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.347 Round 2: 73 peptides, 11 chains. Longest chain 14 peptides. Score 0.501 Round 3: 75 peptides, 11 chains. Longest chain 15 peptides. Score 0.520 Round 4: 78 peptides, 11 chains. Longest chain 13 peptides. Score 0.547 Round 5: 73 peptides, 10 chains. Longest chain 15 peptides. Score 0.542 Taking the results from Round 4 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2307 restraints for refining 997 atoms. 2050 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2670 (Rfree = 0.000) for 997 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 7: After refmac, R = 0.2438 (Rfree = 0.000) for 980 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 8: After refmac, R = 0.2298 (Rfree = 0.000) for 972 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.2154 (Rfree = 0.000) for 966 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2163 (Rfree = 0.000) for 962 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 1023 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 7 peptides. Score 0.362 Round 2: 67 peptides, 9 chains. Longest chain 19 peptides. Score 0.528 Round 3: 60 peptides, 9 chains. Longest chain 14 peptides. Score 0.459 Round 4: 68 peptides, 8 chains. Longest chain 16 peptides. Score 0.578 Round 5: 56 peptides, 6 chains. Longest chain 23 peptides. Score 0.554 Taking the results from Round 4 Chains 8, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2308 restraints for refining 988 atoms. 2076 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2333 (Rfree = 0.000) for 988 atoms. Found 2 (5 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.2174 (Rfree = 0.000) for 975 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 13: After refmac, R = 0.2028 (Rfree = 0.000) for 968 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.1955 (Rfree = 0.000) for 965 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.1788 (Rfree = 0.000) for 961 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 1005 seeds are put forward Round 1: 67 peptides, 10 chains. Longest chain 13 peptides. Score 0.485 Round 2: 77 peptides, 10 chains. Longest chain 17 peptides. Score 0.578 Round 3: 70 peptides, 9 chains. Longest chain 18 peptides. Score 0.556 Round 4: 76 peptides, 10 chains. Longest chain 17 peptides. Score 0.569 Round 5: 82 peptides, 11 chains. Longest chain 17 peptides. Score 0.582 Taking the results from Round 5 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2103 restraints for refining 977 atoms. 1830 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2369 (Rfree = 0.000) for 977 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 17: After refmac, R = 0.1985 (Rfree = 0.000) for 967 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 18: After refmac, R = 0.1931 (Rfree = 0.000) for 966 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.1801 (Rfree = 0.000) for 967 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.1734 (Rfree = 0.000) for 966 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 1000 seeds are put forward Round 1: 57 peptides, 10 chains. Longest chain 12 peptides. Score 0.380 Round 2: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.438 Round 3: 69 peptides, 12 chains. Longest chain 14 peptides. Score 0.417 Round 4: 70 peptides, 11 chains. Longest chain 13 peptides. Score 0.472 Round 5: 67 peptides, 10 chains. Longest chain 11 peptides. Score 0.485 Taking the results from Round 5 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2318 restraints for refining 1013 atoms. 2100 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2325 (Rfree = 0.000) for 1013 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 22: After refmac, R = 0.2328 (Rfree = 0.000) for 1002 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 23: After refmac, R = 0.1964 (Rfree = 0.000) for 994 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 24: After refmac, R = 0.1755 (Rfree = 0.000) for 990 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.1903 (Rfree = 0.000) for 988 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 1018 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 13 peptides. Score 0.325 Round 2: 63 peptides, 10 chains. Longest chain 15 peptides. Score 0.445 Round 3: 69 peptides, 11 chains. Longest chain 20 peptides. Score 0.462 Round 4: 71 peptides, 8 chains. Longest chain 35 peptides. Score 0.603 Round 5: 76 peptides, 11 chains. Longest chain 17 peptides. Score 0.529 Taking the results from Round 4 Chains 8, Residues 63, Estimated correctness of the model 0.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2203 restraints for refining 1003 atoms. 1959 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2369 (Rfree = 0.000) for 1003 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 27: After refmac, R = 0.2103 (Rfree = 0.000) for 998 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 28: After refmac, R = 0.2036 (Rfree = 0.000) for 989 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.1945 (Rfree = 0.000) for 986 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.1873 (Rfree = 0.000) for 986 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 1017 seeds are put forward Round 1: 43 peptides, 8 chains. Longest chain 12 peptides. Score 0.316 Round 2: 61 peptides, 10 chains. Longest chain 14 peptides. Score 0.424 Round 3: 71 peptides, 12 chains. Longest chain 15 peptides. Score 0.438 Round 4: 58 peptides, 9 chains. Longest chain 9 peptides. Score 0.438 Round 5: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.368 Taking the results from Round 4 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2440 restraints for refining 1012 atoms. 2253 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2012 (Rfree = 0.000) for 1012 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.1744 (Rfree = 0.000) for 1003 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.1809 (Rfree = 0.000) for 1001 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.1686 (Rfree = 0.000) for 995 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2126 (Rfree = 0.000) for 992 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.57 Search for helices and strands: 0 residues in 0 chains, 1022 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.297 Round 2: 57 peptides, 9 chains. Longest chain 17 peptides. Score 0.428 Round 3: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.380 Round 4: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.372 Round 5: 59 peptides, 9 chains. Longest chain 19 peptides. Score 0.449 Taking the results from Round 5 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2250 restraints for refining 996 atoms. 2059 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2088 (Rfree = 0.000) for 996 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 37: After refmac, R = 0.1798 (Rfree = 0.000) for 992 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 38: After refmac, R = 0.1704 (Rfree = 0.000) for 989 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.1615 (Rfree = 0.000) for 987 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1615 (Rfree = 0.000) for 984 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1015 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.249 Round 2: 48 peptides, 9 chains. Longest chain 7 peptides. Score 0.325 Round 3: 53 peptides, 9 chains. Longest chain 9 peptides. Score 0.383 Round 4: 47 peptides, 9 chains. Longest chain 9 peptides. Score 0.313 Round 5: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.360 Taking the results from Round 3 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1593 reflections ( 99.75 % complete ) and 2336 restraints for refining 1006 atoms. 2169 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1804 (Rfree = 0.000) for 1006 atoms. Found 3 (5 requested) and removed 12 (2 requested) atoms. Cycle 42: After refmac, R = 0.1531 (Rfree = 0.000) for 993 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.1608 (Rfree = 0.000) for 988 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.1415 (Rfree = 0.000) for 985 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1516 (Rfree = 0.000) for 982 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 1010 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.238 Round 2: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.360 Round 3: 44 peptides, 9 chains. Longest chain 9 peptides. Score 0.275 Round 4: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.278 Round 5: 42 peptides, 8 chains. Longest chain 9 peptides. Score 0.304 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 42, 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 2inb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1593 reflections ( 99.75 % complete ) and 2208 restraints for refining 969 atoms. 2049 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1979 (Rfree = 0.000) for 969 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1896 (Rfree = 0.000) for 966 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1755 (Rfree = 0.000) for 961 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1887 (Rfree = 0.000) for 959 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... TimeTaking 24.72