Sun 23 Dec 22:22:56 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 2aj6-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.4-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/2aj6-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.4-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 22:23:06 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/2aj6-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.4-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: 0.6217 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 159 Adjusted target solvent content: 0.37 Input MTZ file: 2aj6-3.4-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: 23 Cell parameters: 40.044 74.871 90.673 90.000 90.000 90.000 Input sequence file: 2aj6-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1272 target number of atoms Had to go as low as 0.35 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: 28.866 3.400 Wilson plot Bfac: 61.81 2020 reflections ( 98.68 % complete ) and 0 restraints for refining 1415 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.2960 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2559 (Rfree = 0.000) for 1415 atoms. Found 9 (10 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.76 Search for helices and strands: 0 residues in 0 chains, 1426 seeds are put forward Round 1: 49 peptides, 9 chains. Longest chain 11 peptides. Score 0.347 Round 2: 78 peptides, 11 chains. Longest chain 18 peptides. Score 0.568 Round 3: 85 peptides, 10 chains. Longest chain 20 peptides. Score 0.664 Round 4: 84 peptides, 9 chains. Longest chain 21 peptides. Score 0.690 Round 5: 78 peptides, 9 chains. Longest chain 18 peptides. Score 0.645 Taking the results from Round 4 Chains 11, Residues 75, Estimated correctness of the model 55.3 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2462 restraints for refining 1121 atoms. 2093 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2788 (Rfree = 0.000) for 1121 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 2: After refmac, R = 0.2519 (Rfree = 0.000) for 1093 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.2409 (Rfree = 0.000) for 1085 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2393 (Rfree = 0.000) for 1078 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2282 (Rfree = 0.000) for 1078 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.87 Search for helices and strands: 0 residues in 0 chains, 1115 seeds are put forward Round 1: 60 peptides, 9 chains. Longest chain 10 peptides. Score 0.476 Round 2: 74 peptides, 10 chains. Longest chain 20 peptides. Score 0.572 Round 3: 79 peptides, 8 chains. Longest chain 31 peptides. Score 0.688 Round 4: 79 peptides, 11 chains. Longest chain 17 peptides. Score 0.577 Round 5: 75 peptides, 9 chains. Longest chain 20 peptides. Score 0.620 Taking the results from Round 3 Chains 8, Residues 71, Estimated correctness of the model 54.7 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2217 restraints for refining 1113 atoms. 1799 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2385 (Rfree = 0.000) for 1113 atoms. Found 5 (8 requested) and removed 31 (4 requested) atoms. Cycle 7: After refmac, R = 0.2233 (Rfree = 0.000) for 1076 atoms. Found 2 (8 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2176 (Rfree = 0.000) for 1058 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2103 (Rfree = 0.000) for 1047 atoms. Found 2 (7 requested) and removed 9 (3 requested) atoms. Cycle 10: After refmac, R = 0.2082 (Rfree = 0.000) for 1039 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.88 Search for helices and strands: 0 residues in 0 chains, 1089 seeds are put forward Round 1: 68 peptides, 9 chains. Longest chain 20 peptides. Score 0.557 Round 2: 77 peptides, 11 chains. Longest chain 18 peptides. Score 0.558 Round 3: 85 peptides, 12 chains. Longest chain 13 peptides. Score 0.591 Round 4: 85 peptides, 11 chains. Longest chain 14 peptides. Score 0.629 Round 5: 85 peptides, 10 chains. Longest chain 29 peptides. Score 0.664 Taking the results from Round 5 Chains 11, Residues 75, Estimated correctness of the model 48.2 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2134 restraints for refining 1064 atoms. 1720 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2589 (Rfree = 0.000) for 1064 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 12: After refmac, R = 0.2356 (Rfree = 0.000) for 1053 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.2311 (Rfree = 0.000) for 1043 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2228 (Rfree = 0.000) for 1037 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.2152 (Rfree = 0.000) for 1035 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.83 Search for helices and strands: 0 residues in 0 chains, 1069 seeds are put forward Round 1: 73 peptides, 13 chains. Longest chain 13 peptides. Score 0.429 Round 2: 69 peptides, 10 chains. Longest chain 16 peptides. Score 0.524 Round 3: 69 peptides, 10 chains. Longest chain 11 peptides. Score 0.524 Round 4: 70 peptides, 9 chains. Longest chain 16 peptides. Score 0.576 Round 5: 68 peptides, 9 chains. Longest chain 14 peptides. Score 0.557 Taking the results from Round 4 Chains 9, Residues 61, Estimated correctness of the model 20.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2548 restraints for refining 1048 atoms. 2313 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2371 (Rfree = 0.000) for 1048 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 17: After refmac, R = 0.2112 (Rfree = 0.000) for 1048 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2053 (Rfree = 0.000) for 1042 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.1969 (Rfree = 0.000) for 1038 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1954 (Rfree = 0.000) for 1035 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.93 Search for helices and strands: 0 residues in 0 chains, 1067 seeds are put forward Round 1: 72 peptides, 11 chains. Longest chain 13 peptides. Score 0.510 Round 2: 72 peptides, 10 chains. Longest chain 19 peptides. Score 0.553 Round 3: 78 peptides, 11 chains. Longest chain 16 peptides. Score 0.568 Round 4: 72 peptides, 10 chains. Longest chain 16 peptides. Score 0.553 Round 5: 78 peptides, 11 chains. Longest chain 13 peptides. Score 0.568 Taking the results from Round 5 Chains 11, Residues 67, Estimated correctness of the model 17.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2342 restraints for refining 1036 atoms. 2085 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2471 (Rfree = 0.000) for 1036 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 22: After refmac, R = 0.2292 (Rfree = 0.000) for 1039 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2233 (Rfree = 0.000) for 1041 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2196 (Rfree = 0.000) for 1045 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2186 (Rfree = 0.000) for 1043 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.96 Search for helices and strands: 0 residues in 0 chains, 1086 seeds are put forward Round 1: 60 peptides, 10 chains. Longest chain 13 peptides. Score 0.427 Round 2: 75 peptides, 12 chains. Longest chain 9 peptides. Score 0.496 Round 3: 76 peptides, 12 chains. Longest chain 10 peptides. Score 0.506 Round 4: 74 peptides, 11 chains. Longest chain 10 peptides. Score 0.530 Round 5: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.479 Taking the results from Round 4 Chains 11, Residues 63, Estimated correctness of the model 4.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2562 restraints for refining 1062 atoms. 2321 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2489 (Rfree = 0.000) for 1062 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2305 (Rfree = 0.000) for 1057 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.2026 (Rfree = 0.000) for 1051 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2010 (Rfree = 0.000) for 1049 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.1900 (Rfree = 0.000) for 1050 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.88 Search for helices and strands: 0 residues in 0 chains, 1091 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.389 Round 2: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.457 Round 3: 66 peptides, 11 chains. Longest chain 8 peptides. Score 0.446 Round 4: 68 peptides, 9 chains. Longest chain 13 peptides. Score 0.557 Round 5: 67 peptides, 10 chains. Longest chain 10 peptides. Score 0.503 Taking the results from Round 4 Chains 9, Residues 59, Estimated correctness of the model 14.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2539 restraints for refining 1066 atoms. 2312 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2007 (Rfree = 0.000) for 1066 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.2249 (Rfree = 0.000) for 1057 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.1935 (Rfree = 0.000) for 1052 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2065 (Rfree = 0.000) for 1048 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1820 (Rfree = 0.000) for 1047 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.75 Search for helices and strands: 0 residues in 0 chains, 1088 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.356 Round 2: 63 peptides, 9 chains. Longest chain 11 peptides. Score 0.507 Round 3: 67 peptides, 10 chains. Longest chain 12 peptides. Score 0.503 Round 4: 64 peptides, 9 chains. Longest chain 13 peptides. Score 0.518 Round 5: 71 peptides, 10 chains. Longest chain 14 peptides. Score 0.543 Taking the results from Round 5 Chains 10, Residues 61, Estimated correctness of the model 9.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2598 restraints for refining 1090 atoms. 2364 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1826 (Rfree = 0.000) for 1090 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 37: After refmac, R = 0.1638 (Rfree = 0.000) for 1084 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.1542 (Rfree = 0.000) for 1083 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.1767 (Rfree = 0.000) for 1079 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1775 (Rfree = 0.000) for 1072 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.88 Search for helices and strands: 0 residues in 0 chains, 1126 seeds are put forward Round 1: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.396 Round 2: 54 peptides, 9 chains. Longest chain 9 peptides. Score 0.408 Round 3: 58 peptides, 8 chains. Longest chain 10 peptides. Score 0.502 Round 4: 59 peptides, 9 chains. Longest chain 10 peptides. Score 0.465 Round 5: 49 peptides, 8 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 3 Chains 8, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2020 reflections ( 98.68 % complete ) and 2618 restraints for refining 1072 atoms. 2426 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2258 (Rfree = 0.000) for 1072 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2170 (Rfree = 0.000) for 1066 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.1952 (Rfree = 0.000) for 1061 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.1875 (Rfree = 0.000) for 1054 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.1378 (Rfree = 0.000) for 1052 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.83 Search for helices and strands: 0 residues in 0 chains, 1090 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 10 peptides. Score 0.292 Round 2: 53 peptides, 8 chains. Longest chain 10 peptides. Score 0.447 Round 3: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.408 Round 4: 43 peptides, 7 chains. Longest chain 10 peptides. Score 0.381 Round 5: 51 peptides, 8 chains. Longest chain 10 peptides. Score 0.424 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 45, 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 2aj6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2020 reflections ( 98.68 % complete ) and 2528 restraints for refining 1058 atoms. 2356 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2007 (Rfree = 0.000) for 1058 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1910 (Rfree = 0.000) for 1052 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1828 (Rfree = 0.000) for 1047 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1902 (Rfree = 0.000) for 1042 atoms. TimeTaking 25