Sun 23 Dec 22:23:10 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 2fcl-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fcl-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.2-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/2fcl-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.2-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 22:23:20 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/2fcl-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fcl-3.2-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: 0.5955 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 169 Adjusted target solvent content: 0.48 Input MTZ file: 2fcl-3.2-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: 1 Cell parameters: 32.560 36.210 39.280 74.110 86.380 79.700 Input sequence file: 2fcl-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1352 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.656 3.200 Wilson plot Bfac: 50.07 2743 reflections ( 97.93 % complete ) and 0 restraints for refining 1500 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3090 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3105 (Rfree = 0.000) for 1500 atoms. Found 6 (13 requested) and removed 199 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.77 2.84 Search for helices and strands: 0 residues in 0 chains, 1312 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.180 Round 2: 53 peptides, 12 chains. Longest chain 6 peptides. Score 0.223 Round 3: 66 peptides, 14 chains. Longest chain 6 peptides. Score 0.273 Round 4: 60 peptides, 11 chains. Longest chain 7 peptides. Score 0.340 Round 5: 56 peptides, 10 chains. Longest chain 12 peptides. Score 0.343 Taking the results from Round 5 Chains 10, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2793 restraints for refining 1234 atoms. 2619 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3589 (Rfree = 0.000) for 1234 atoms. Found 11 (11 requested) and removed 55 (5 requested) atoms. Cycle 2: After refmac, R = 0.3143 (Rfree = 0.000) for 1179 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 3: After refmac, R = 0.3225 (Rfree = 0.000) for 1163 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2831 (Rfree = 0.000) for 1159 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2798 (Rfree = 0.000) for 1157 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.73 2.80 Search for helices and strands: 0 residues in 0 chains, 1197 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 5 peptides. Score 0.200 Round 2: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.297 Round 3: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.357 Round 4: 81 peptides, 15 chains. Longest chain 11 peptides. Score 0.378 Round 5: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.387 Taking the results from Round 5 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2479 restraints for refining 1132 atoms. 2226 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2765 (Rfree = 0.000) for 1132 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 7: After refmac, R = 0.2756 (Rfree = 0.000) for 1123 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.2670 (Rfree = 0.000) for 1120 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2699 (Rfree = 0.000) for 1119 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2745 (Rfree = 0.000) for 1114 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.92 3.00 Search for helices and strands: 0 residues in 0 chains, 1153 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 8 peptides. Score 0.232 Round 2: 76 peptides, 14 chains. Longest chain 11 peptides. Score 0.371 Round 3: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.445 Round 4: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.460 Round 5: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.451 Taking the results from Round 4 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2300 restraints for refining 1120 atoms. 2026 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2872 (Rfree = 0.000) for 1120 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2437 (Rfree = 0.000) for 1113 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2985 (Rfree = 0.000) for 1105 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2754 (Rfree = 0.000) for 1101 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.3012 (Rfree = 0.000) for 1101 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.97 3.05 Search for helices and strands: 0 residues in 0 chains, 1143 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 7 peptides. Score 0.229 Round 2: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.387 Round 3: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.385 Round 4: 83 peptides, 15 chains. Longest chain 12 peptides. Score 0.396 Round 5: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.373 Taking the results from Round 4 Chains 15, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2569 restraints for refining 1176 atoms. 2312 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3319 (Rfree = 0.000) for 1176 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 17: After refmac, R = 0.3199 (Rfree = 0.000) for 1150 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 18: After refmac, R = 0.2825 (Rfree = 0.000) for 1138 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2819 (Rfree = 0.000) for 1135 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2709 (Rfree = 0.000) for 1136 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 2.99 Search for helices and strands: 0 residues in 0 chains, 1179 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.297 Round 2: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.313 Round 3: 76 peptides, 15 chains. Longest chain 7 peptides. Score 0.331 Round 4: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.369 Round 5: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.398 Taking the results from Round 5 Chains 14, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2576 restraints for refining 1171 atoms. 2330 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3540 (Rfree = 0.000) for 1171 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 22: After refmac, R = 0.3331 (Rfree = 0.000) for 1157 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.3299 (Rfree = 0.000) for 1156 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 24: After refmac, R = 0.3245 (Rfree = 0.000) for 1146 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.2912 (Rfree = 0.000) for 1143 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 3.12 Search for helices and strands: 0 residues in 0 chains, 1190 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 5 peptides. Score 0.211 Round 2: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.329 Round 3: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.371 Round 4: 80 peptides, 15 chains. Longest chain 12 peptides. Score 0.369 Round 5: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.373 Taking the results from Round 5 Chains 13, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2375 restraints for refining 1153 atoms. 2152 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3098 (Rfree = 0.000) for 1153 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.3319 (Rfree = 0.000) for 1142 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.3159 (Rfree = 0.000) for 1134 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.3073 (Rfree = 0.000) for 1128 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.3306 (Rfree = 0.000) for 1128 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.55 2.62 Search for helices and strands: 0 residues in 0 chains, 1178 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 5 peptides. Score 0.201 Round 2: 53 peptides, 11 chains. Longest chain 6 peptides. Score 0.268 Round 3: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.279 Round 4: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.285 Round 5: 64 peptides, 13 chains. Longest chain 9 peptides. Score 0.295 Taking the results from Round 5 Chains 13, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2482 restraints for refining 1141 atoms. 2291 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3291 (Rfree = 0.000) for 1141 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 32: After refmac, R = 0.3182 (Rfree = 0.000) for 1132 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 33: After refmac, R = 0.2982 (Rfree = 0.000) for 1126 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2435 (Rfree = 0.000) for 1123 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2228 (Rfree = 0.000) for 1127 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.95 3.03 Search for helices and strands: 0 residues in 0 chains, 1164 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.180 Round 2: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.228 Round 3: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.300 Round 4: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.295 Round 5: 51 peptides, 10 chains. Longest chain 9 peptides. Score 0.292 Taking the results from Round 3 Chains 11, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2370 restraints for refining 1083 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3518 (Rfree = 0.000) for 1083 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 37: After refmac, R = 0.3175 (Rfree = 0.000) for 1079 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 38: After refmac, R = 0.2971 (Rfree = 0.000) for 1070 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.3171 (Rfree = 0.000) for 1066 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.3345 (Rfree = 0.000) for 1065 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.55 2.62 Search for helices and strands: 0 residues in 0 chains, 1100 seeds are put forward Round 1: 30 peptides, 7 chains. Longest chain 6 peptides. Score 0.194 Round 2: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.214 Round 3: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.237 Round 4: 48 peptides, 11 chains. Longest chain 6 peptides. Score 0.213 Round 5: 48 peptides, 10 chains. Longest chain 10 peptides. Score 0.260 Taking the results from Round 5 Chains 10, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2743 reflections ( 97.93 % complete ) and 2293 restraints for refining 1062 atoms. 2151 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3282 (Rfree = 0.000) for 1062 atoms. Found 4 (9 requested) and removed 15 (4 requested) atoms. Cycle 42: After refmac, R = 0.3302 (Rfree = 0.000) for 1043 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 43: After refmac, R = 0.3196 (Rfree = 0.000) for 1037 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.3416 (Rfree = 0.000) for 1035 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.3305 (Rfree = 0.000) for 1028 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.62 2.69 Search for helices and strands: 0 residues in 0 chains, 1057 seeds are put forward Round 1: 41 peptides, 10 chains. Longest chain 5 peptides. Score 0.179 Round 2: 54 peptides, 12 chains. Longest chain 8 peptides. Score 0.234 Round 3: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.191 Round 4: 45 peptides, 10 chains. Longest chain 7 peptides. Score 0.226 Round 5: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.260 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, 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 2fcl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2743 reflections ( 97.93 % complete ) and 2060 restraints for refining 987 atoms. 1918 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3448 (Rfree = 0.000) for 987 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3472 (Rfree = 0.000) for 981 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3718 (Rfree = 0.000) for 972 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3558 (Rfree = 0.000) for 963 atoms. TimeTaking 24.14