null Sun 23 Dec 22:22:55 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 1vjv-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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/1vjv-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 22:23:04 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/1vjv-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 333 and 0 Target number of residues in the AU: 333 Target solvent content: 0.5846 Checking the provided sequence file Detected sequence length: 415 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 415 Adjusted target solvent content: 0.48 Input MTZ file: 1vjv-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: 19 Cell parameters: 49.299 81.862 107.491 90.000 90.000 90.000 Input sequence file: 1vjv-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3320 target number of atoms Had to go as low as 0.55 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: 65.126 3.400 Wilson plot Bfac: 46.41 6181 reflections ( 96.90 % complete ) and 0 restraints for refining 3661 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.2894 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2914 (Rfree = 0.000) for 3661 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward Round 1: 192 peptides, 32 chains. Longest chain 16 peptides. Score 0.427 Round 2: 224 peptides, 26 chains. Longest chain 27 peptides. Score 0.612 Round 3: 239 peptides, 28 chains. Longest chain 20 peptides. Score 0.627 Round 4: 247 peptides, 25 chains. Longest chain 27 peptides. Score 0.681 Round 5: 225 peptides, 26 chains. Longest chain 24 peptides. Score 0.615 Taking the results from Round 4 Chains 27, Residues 222, Estimated correctness of the model 52.9 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6427 restraints for refining 3017 atoms. 5442 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2584 (Rfree = 0.000) for 3017 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. Cycle 2: After refmac, R = 0.2433 (Rfree = 0.000) for 2943 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 3: After refmac, R = 0.2275 (Rfree = 0.000) for 2912 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 4: After refmac, R = 0.2227 (Rfree = 0.000) for 2890 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 5: After refmac, R = 0.2191 (Rfree = 0.000) for 2885 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 2990 seeds are put forward Round 1: 215 peptides, 29 chains. Longest chain 18 peptides. Score 0.547 Round 2: 237 peptides, 31 chains. Longest chain 24 peptides. Score 0.585 Round 3: 244 peptides, 26 chains. Longest chain 24 peptides. Score 0.663 Round 4: 245 peptides, 30 chains. Longest chain 32 peptides. Score 0.619 Round 5: 255 peptides, 29 chains. Longest chain 18 peptides. Score 0.656 Taking the results from Round 3 Chains 28, Residues 218, Estimated correctness of the model 47.9 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6441 restraints for refining 3003 atoms. 5408 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2415 (Rfree = 0.000) for 3003 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 7: After refmac, R = 0.2178 (Rfree = 0.000) for 2949 atoms. Found 19 (22 requested) and removed 19 (11 requested) atoms. Cycle 8: After refmac, R = 0.2107 (Rfree = 0.000) for 2922 atoms. Found 13 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2072 (Rfree = 0.000) for 2906 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.2073 (Rfree = 0.000) for 2898 atoms. Found 15 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.16 Search for helices and strands: 0 residues in 0 chains, 2977 seeds are put forward Round 1: 221 peptides, 32 chains. Longest chain 17 peptides. Score 0.524 Round 2: 219 peptides, 27 chains. Longest chain 18 peptides. Score 0.585 Round 3: 233 peptides, 29 chains. Longest chain 21 peptides. Score 0.599 Round 4: 251 peptides, 31 chains. Longest chain 24 peptides. Score 0.623 Round 5: 252 peptides, 29 chains. Longest chain 24 peptides. Score 0.649 Taking the results from Round 5 Chains 29, Residues 223, Estimated correctness of the model 43.8 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6622 restraints for refining 2966 atoms. 5660 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2480 (Rfree = 0.000) for 2966 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 12: After refmac, R = 0.2312 (Rfree = 0.000) for 2951 atoms. Found 18 (22 requested) and removed 18 (11 requested) atoms. Cycle 13: After refmac, R = 0.2196 (Rfree = 0.000) for 2942 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2175 (Rfree = 0.000) for 2934 atoms. Found 4 (22 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2114 (Rfree = 0.000) for 2916 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 3.13 Search for helices and strands: 0 residues in 0 chains, 2981 seeds are put forward Round 1: 202 peptides, 30 chains. Longest chain 14 peptides. Score 0.492 Round 2: 233 peptides, 31 chains. Longest chain 24 peptides. Score 0.574 Round 3: 231 peptides, 27 chains. Longest chain 26 peptides. Score 0.618 Round 4: 230 peptides, 29 chains. Longest chain 27 peptides. Score 0.591 Round 5: 224 peptides, 30 chains. Longest chain 28 peptides. Score 0.560 Taking the results from Round 3 Chains 29, Residues 204, Estimated correctness of the model 34.4 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6442 restraints for refining 2973 atoms. 5489 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2795 (Rfree = 0.000) for 2973 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 17: After refmac, R = 0.2425 (Rfree = 0.000) for 2945 atoms. Found 20 (22 requested) and removed 18 (11 requested) atoms. Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 2922 atoms. Found 20 (22 requested) and removed 16 (11 requested) atoms. Cycle 19: After refmac, R = 0.2241 (Rfree = 0.000) for 2913 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.2176 (Rfree = 0.000) for 2902 atoms. Found 14 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 2986 seeds are put forward Round 1: 208 peptides, 31 chains. Longest chain 15 peptides. Score 0.497 Round 2: 229 peptides, 29 chains. Longest chain 22 peptides. Score 0.588 Round 3: 228 peptides, 32 chains. Longest chain 19 peptides. Score 0.546 Round 4: 222 peptides, 29 chains. Longest chain 18 peptides. Score 0.568 Round 5: 230 peptides, 28 chains. Longest chain 22 peptides. Score 0.603 Taking the results from Round 5 Chains 29, Residues 202, Estimated correctness of the model 29.7 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6443 restraints for refining 3019 atoms. 5510 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2460 (Rfree = 0.000) for 3019 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 22: After refmac, R = 0.2268 (Rfree = 0.000) for 2998 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 23: After refmac, R = 0.2146 (Rfree = 0.000) for 2990 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.2069 (Rfree = 0.000) for 2989 atoms. Found 20 (22 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.2051 (Rfree = 0.000) for 2994 atoms. Found 17 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 3074 seeds are put forward Round 1: 195 peptides, 33 chains. Longest chain 12 peptides. Score 0.422 Round 2: 220 peptides, 29 chains. Longest chain 21 peptides. Score 0.562 Round 3: 212 peptides, 32 chains. Longest chain 22 peptides. Score 0.496 Round 4: 209 peptides, 29 chains. Longest chain 19 peptides. Score 0.528 Round 5: 220 peptides, 25 chains. Longest chain 29 peptides. Score 0.614 Taking the results from Round 5 Chains 27, Residues 195, Estimated correctness of the model 33.2 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6634 restraints for refining 3019 atoms. 5788 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2313 (Rfree = 0.000) for 3019 atoms. Found 20 (22 requested) and removed 20 (11 requested) atoms. Cycle 27: After refmac, R = 0.2075 (Rfree = 0.000) for 3003 atoms. Found 17 (22 requested) and removed 16 (11 requested) atoms. Cycle 28: After refmac, R = 0.2058 (Rfree = 0.000) for 2991 atoms. Found 12 (22 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.1975 (Rfree = 0.000) for 2985 atoms. Found 19 (22 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1973 (Rfree = 0.000) for 2985 atoms. Found 14 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 3.12 Search for helices and strands: 0 residues in 0 chains, 3056 seeds are put forward Round 1: 183 peptides, 31 chains. Longest chain 11 peptides. Score 0.410 Round 2: 194 peptides, 25 chains. Longest chain 24 peptides. Score 0.538 Round 3: 205 peptides, 28 chains. Longest chain 16 peptides. Score 0.530 Round 4: 187 peptides, 28 chains. Longest chain 13 peptides. Score 0.471 Round 5: 203 peptides, 28 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 2 Chains 25, Residues 169, Estimated correctness of the model 7.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 7152 restraints for refining 3019 atoms. 6501 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2128 (Rfree = 0.000) for 3019 atoms. Found 18 (22 requested) and removed 17 (11 requested) atoms. Cycle 32: After refmac, R = 0.2033 (Rfree = 0.000) for 3017 atoms. Found 16 (22 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.1993 (Rfree = 0.000) for 3018 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1971 (Rfree = 0.000) for 3016 atoms. Found 6 (22 requested) and removed 15 (11 requested) atoms. Cycle 35: After refmac, R = 0.1878 (Rfree = 0.000) for 3004 atoms. Found 6 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 3.15 Search for helices and strands: 0 residues in 0 chains, 3064 seeds are put forward Round 1: 199 peptides, 33 chains. Longest chain 20 peptides. Score 0.437 Round 2: 205 peptides, 29 chains. Longest chain 16 peptides. Score 0.516 Round 3: 214 peptides, 29 chains. Longest chain 25 peptides. Score 0.544 Round 4: 216 peptides, 27 chains. Longest chain 21 peptides. Score 0.577 Round 5: 222 peptides, 30 chains. Longest chain 24 peptides. Score 0.555 Taking the results from Round 4 Chains 29, Residues 189, Estimated correctness of the model 21.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6829 restraints for refining 3017 atoms. 6071 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2231 (Rfree = 0.000) for 3017 atoms. Found 17 (22 requested) and removed 21 (11 requested) atoms. Cycle 37: After refmac, R = 0.2042 (Rfree = 0.000) for 3007 atoms. Found 19 (22 requested) and removed 12 (11 requested) atoms. Cycle 38: After refmac, R = 0.1891 (Rfree = 0.000) for 3007 atoms. Found 12 (22 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1876 (Rfree = 0.000) for 3007 atoms. Found 7 (22 requested) and removed 15 (11 requested) atoms. Cycle 40: After refmac, R = 0.1714 (Rfree = 0.000) for 2993 atoms. Found 4 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 3.13 Search for helices and strands: 0 residues in 0 chains, 3048 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 12 peptides. Score 0.403 Round 2: 180 peptides, 27 chains. Longest chain 20 peptides. Score 0.462 Round 3: 201 peptides, 27 chains. Longest chain 20 peptides. Score 0.531 Round 4: 206 peptides, 27 chains. Longest chain 19 peptides. Score 0.547 Round 5: 207 peptides, 28 chains. Longest chain 21 peptides. Score 0.536 Taking the results from Round 4 Chains 27, Residues 179, Estimated correctness of the model 10.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6181 reflections ( 96.90 % complete ) and 6715 restraints for refining 3019 atoms. 5969 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2205 (Rfree = 0.000) for 3019 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 42: After refmac, R = 0.1984 (Rfree = 0.000) for 3005 atoms. Found 17 (22 requested) and removed 16 (11 requested) atoms. Cycle 43: After refmac, R = 0.1897 (Rfree = 0.000) for 2997 atoms. Found 10 (22 requested) and removed 17 (11 requested) atoms. Cycle 44: After refmac, R = 0.1761 (Rfree = 0.000) for 2989 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1752 (Rfree = 0.000) for 2981 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 3054 seeds are put forward Round 1: 163 peptides, 31 chains. Longest chain 11 peptides. Score 0.334 Round 2: 187 peptides, 29 chains. Longest chain 18 peptides. Score 0.456 Round 3: 178 peptides, 26 chains. Longest chain 19 peptides. Score 0.470 Round 4: 186 peptides, 26 chains. Longest chain 31 peptides. Score 0.497 Round 5: 170 peptides, 26 chains. Longest chain 19 peptides. Score 0.442 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 160, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1vjv-3_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (160 residues) following loop building 3 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6181 reflections ( 96.90 % complete ) and 6802 restraints for refining 3019 atoms. 6093 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2196 (Rfree = 0.000) for 3019 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2253 (Rfree = 0.000) for 2994 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2110 (Rfree = 0.000) for 2975 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2107 (Rfree = 0.000) for 2957 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:15:31 GMT 2018 Job finished. TimeTaking 52.6 Used memory is bytes: 10900816