Sun 23 Dec 22:23:05 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 2o2g-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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/2o2g-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 22:23:15 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/2o2g-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 131 and 0 Target number of residues in the AU: 131 Target solvent content: 0.6513 Checking the provided sequence file Detected sequence length: 223 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 223 Adjusted target solvent content: 0.41 Input MTZ file: 2o2g-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: 19 Cell parameters: 47.887 62.444 67.988 90.000 90.000 90.000 Input sequence file: 2o2g-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1784 target number of atoms Had to go as low as 0.60 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: 45.990 3.801 Wilson plot Bfac: 78.77 2164 reflections ( 97.96 % complete ) and 0 restraints for refining 1978 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3755 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3854 (Rfree = 0.000) for 1978 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 4.29 Search for helices and strands: 0 residues in 0 chains, 1992 seeds are put forward Round 1: 29 peptides, 6 chains. Longest chain 6 peptides. Score 0.231 Round 2: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.235 Round 3: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.268 Round 4: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.287 Round 5: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 5 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 4178 restraints for refining 1613 atoms. 4011 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3555 (Rfree = 0.000) for 1613 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.3443 (Rfree = 0.000) for 1594 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 3: After refmac, R = 0.3494 (Rfree = 0.000) for 1573 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.3294 (Rfree = 0.000) for 1562 atoms. Found 7 (8 requested) and removed 17 (4 requested) atoms. Cycle 5: After refmac, R = 0.2853 (Rfree = 0.000) for 1542 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 4.12 Search for helices and strands: 0 residues in 0 chains, 1575 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.237 Round 2: 79 peptides, 15 chains. Longest chain 11 peptides. Score 0.339 Round 3: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.296 Round 4: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.360 Round 5: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 5 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 3103 restraints for refining 1351 atoms. 2887 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3249 (Rfree = 0.000) for 1351 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.3337 (Rfree = 0.000) for 1338 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.3122 (Rfree = 0.000) for 1333 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 9: After refmac, R = 0.3083 (Rfree = 0.000) for 1326 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.2954 (Rfree = 0.000) for 1323 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 4.11 Search for helices and strands: 0 residues in 0 chains, 1353 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.188 Round 2: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.284 Round 3: 68 peptides, 14 chains. Longest chain 10 peptides. Score 0.280 Round 4: 61 peptides, 12 chains. Longest chain 10 peptides. Score 0.293 Round 5: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.253 Taking the results from Round 4 Chains 12, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 2654 restraints for refining 1187 atoms. 2470 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3320 (Rfree = 0.000) for 1187 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.3133 (Rfree = 0.000) for 1173 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.3020 (Rfree = 0.000) for 1165 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.3215 (Rfree = 0.000) for 1159 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.3445 (Rfree = 0.000) for 1152 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 4.14 Search for helices and strands: 0 residues in 0 chains, 1181 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.266 Round 2: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.363 Round 3: 66 peptides, 11 chains. Longest chain 14 peptides. Score 0.375 Round 4: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.383 Round 5: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 5 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 2300 restraints for refining 1132 atoms. 2051 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3442 (Rfree = 0.000) for 1132 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 17: After refmac, R = 0.2936 (Rfree = 0.000) for 1108 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.3001 (Rfree = 0.000) for 1105 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.3081 (Rfree = 0.000) for 1098 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 20: After refmac, R = 0.2960 (Rfree = 0.000) for 1087 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 4.11 Search for helices and strands: 0 residues in 0 chains, 1124 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 6 peptides. Score 0.282 Round 2: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.447 Round 3: 68 peptides, 11 chains. Longest chain 9 peptides. Score 0.391 Round 4: 71 peptides, 10 chains. Longest chain 12 peptides. Score 0.451 Round 5: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.383 Taking the results from Round 4 Chains 10, Residues 61, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 2146 restraints for refining 1104 atoms. 1884 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3537 (Rfree = 0.000) for 1104 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 22: After refmac, R = 0.3333 (Rfree = 0.000) for 1072 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.3483 (Rfree = 0.000) for 1064 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 24: After refmac, R = 0.2953 (Rfree = 0.000) for 1049 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.3249 (Rfree = 0.000) for 1048 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 1069 seeds are put forward Round 1: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.326 Round 2: 63 peptides, 10 chains. Longest chain 9 peptides. Score 0.387 Round 3: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.427 Round 4: 72 peptides, 10 chains. Longest chain 15 peptides. Score 0.458 Round 5: 71 peptides, 11 chains. Longest chain 11 peptides. Score 0.416 Taking the results from Round 4 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 2247 restraints for refining 1069 atoms. 2009 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3522 (Rfree = 0.000) for 1069 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 27: After refmac, R = 0.3334 (Rfree = 0.000) for 1050 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 28: After refmac, R = 0.3272 (Rfree = 0.000) for 1029 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 29: After refmac, R = 0.3078 (Rfree = 0.000) for 1017 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.2991 (Rfree = 0.000) for 1012 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 4.13 Search for helices and strands: 0 residues in 0 chains, 1040 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 10 peptides. Score 0.299 Round 2: 61 peptides, 9 chains. Longest chain 14 peptides. Score 0.407 Round 3: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.323 Round 4: 61 peptides, 12 chains. Longest chain 7 peptides. Score 0.293 Round 5: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.323 Taking the results from Round 2 Chains 9, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 2124 restraints for refining 1006 atoms. 1925 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3498 (Rfree = 0.000) for 1006 atoms. Found 5 (5 requested) and removed 25 (2 requested) atoms. Cycle 32: After refmac, R = 0.3346 (Rfree = 0.000) for 975 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 33: After refmac, R = 0.2814 (Rfree = 0.000) for 971 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.3203 (Rfree = 0.000) for 968 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 35: After refmac, R = 0.3005 (Rfree = 0.000) for 965 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 4.11 Search for helices and strands: 0 residues in 0 chains, 1001 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.245 Round 2: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.302 Round 3: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.273 Round 4: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.332 Round 5: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.314 Taking the results from Round 4 Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 2150 restraints for refining 1005 atoms. 1961 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3372 (Rfree = 0.000) for 1005 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.3154 (Rfree = 0.000) for 997 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.3145 (Rfree = 0.000) for 995 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.3036 (Rfree = 0.000) for 991 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.2963 (Rfree = 0.000) for 988 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 4.06 Search for helices and strands: 0 residues in 0 chains, 1028 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.201 Round 2: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.287 Round 3: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.366 Round 4: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.329 Round 5: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.352 Taking the results from Round 3 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 97.96 % complete ) and 2097 restraints for refining 1028 atoms. 1892 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3471 (Rfree = 0.000) for 1028 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 42: After refmac, R = 0.3061 (Rfree = 0.000) for 1019 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2929 (Rfree = 0.000) for 1017 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.3117 (Rfree = 0.000) for 1015 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.3002 (Rfree = 0.000) for 1006 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 4.11 Search for helices and strands: 0 residues in 0 chains, 1046 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.239 Round 2: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.239 Round 3: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.315 Round 4: 48 peptides, 9 chains. Longest chain 9 peptides. Score 0.293 Round 5: 45 peptides, 8 chains. Longest chain 10 peptides. Score 0.306 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 38, 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 2o2g-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2164 reflections ( 97.96 % complete ) and 2293 restraints for refining 1020 atoms. 2149 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3295 (Rfree = 0.000) for 1020 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3163 (Rfree = 0.000) for 1018 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3122 (Rfree = 0.000) for 1010 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.3274 (Rfree = 0.000) for 1007 atoms. TimeTaking 24.88