Mon 24 Dec 00:09:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmf-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:09:10 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-mrncs/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 326 and 0 Target number of residues in the AU: 326 Target solvent content: 0.6119 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 435 Adjusted target solvent content: 0.48 Input MTZ file: 1vmf-3.4-parrot-mrncs.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: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.65 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 67.531 3.400 Wilson plot Bfac: 57.67 6666 reflections ( 99.72 % complete ) and 0 restraints for refining 3854 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.2972 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2902 (Rfree = 0.000) for 3854 atoms. Found 29 (29 requested) and removed 42 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.30 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 0 residues added, 3903 seeds are put forward Round 1: 186 peptides, 35 chains. Longest chain 13 peptides. Score 0.351 Round 2: 256 peptides, 40 chains. Longest chain 15 peptides. Score 0.513 Round 3: 268 peptides, 37 chains. Longest chain 18 peptides. Score 0.584 Round 4: 270 peptides, 36 chains. Longest chain 18 peptides. Score 0.600 Round 5: 285 peptides, 35 chains. Longest chain 19 peptides. Score 0.648 Taking the results from Round 5 Chains 35, Residues 250, Estimated correctness of the model 43.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6853 restraints for refining 3163 atoms. 5888 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2698 (Rfree = 0.000) for 3163 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 2: After refmac, R = 0.2486 (Rfree = 0.000) for 3104 atoms. Found 18 (23 requested) and removed 23 (11 requested) atoms. Cycle 3: After refmac, R = 0.2360 (Rfree = 0.000) for 3085 atoms. Found 12 (23 requested) and removed 16 (11 requested) atoms. Cycle 4: After refmac, R = 0.2373 (Rfree = 0.000) for 3071 atoms. Found 15 (23 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.2141 (Rfree = 0.000) for 3069 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 3153 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3165 seeds are put forward Round 1: 259 peptides, 41 chains. Longest chain 15 peptides. Score 0.509 Round 2: 291 peptides, 38 chains. Longest chain 15 peptides. Score 0.631 Round 3: 305 peptides, 33 chains. Longest chain 23 peptides. Score 0.711 Round 4: 295 peptides, 32 chains. Longest chain 23 peptides. Score 0.700 Round 5: 288 peptides, 33 chains. Longest chain 21 peptides. Score 0.675 Taking the results from Round 3 Chains 33, Residues 272, Estimated correctness of the model 60.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6746 restraints for refining 3116 atoms. 5691 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2364 (Rfree = 0.000) for 3116 atoms. Found 21 (23 requested) and removed 19 (11 requested) atoms. Cycle 7: After refmac, R = 0.2233 (Rfree = 0.000) for 3098 atoms. Found 14 (23 requested) and removed 14 (11 requested) atoms. Cycle 8: After refmac, R = 0.2026 (Rfree = 0.000) for 3090 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2111 (Rfree = 0.000) for 3086 atoms. Found 8 (22 requested) and removed 16 (11 requested) atoms. Cycle 10: After refmac, R = 0.2042 (Rfree = 0.000) for 3077 atoms. Found 7 (21 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 3199 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 3210 seeds are put forward Round 1: 260 peptides, 37 chains. Longest chain 16 peptides. Score 0.562 Round 2: 283 peptides, 30 chains. Longest chain 19 peptides. Score 0.694 Round 3: 280 peptides, 32 chains. Longest chain 23 peptides. Score 0.668 Round 4: 287 peptides, 28 chains. Longest chain 24 peptides. Score 0.721 Round 5: 287 peptides, 33 chains. Longest chain 32 peptides. Score 0.673 Taking the results from Round 4 Chains 30, Residues 259, Estimated correctness of the model 63.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6943 restraints for refining 3164 atoms. 5894 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2375 (Rfree = 0.000) for 3164 atoms. Found 17 (21 requested) and removed 18 (11 requested) atoms. Cycle 12: After refmac, R = 0.2288 (Rfree = 0.000) for 3153 atoms. Found 7 (20 requested) and removed 15 (11 requested) atoms. Cycle 13: After refmac, R = 0.2197 (Rfree = 0.000) for 3140 atoms. Found 11 (20 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.2258 (Rfree = 0.000) for 3124 atoms. Found 11 (19 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2098 (Rfree = 0.000) for 3114 atoms. Found 3 (19 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 3186 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3199 seeds are put forward Round 1: 256 peptides, 36 chains. Longest chain 19 peptides. Score 0.563 Round 2: 275 peptides, 34 chains. Longest chain 18 peptides. Score 0.635 Round 3: 265 peptides, 27 chains. Longest chain 32 peptides. Score 0.686 Round 4: 255 peptides, 29 chains. Longest chain 17 peptides. Score 0.642 Round 5: 259 peptides, 27 chains. Longest chain 21 peptides. Score 0.673 Taking the results from Round 3 Chains 27, Residues 238, Estimated correctness of the model 54.2 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6962 restraints for refining 3164 atoms. 5979 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2209 (Rfree = 0.000) for 3164 atoms. Found 16 (18 requested) and removed 15 (11 requested) atoms. Cycle 17: After refmac, R = 0.2045 (Rfree = 0.000) for 3155 atoms. Found 7 (18 requested) and removed 12 (11 requested) atoms. Cycle 18: After refmac, R = 0.2001 (Rfree = 0.000) for 3144 atoms. Found 6 (18 requested) and removed 13 (11 requested) atoms. Cycle 19: After refmac, R = 0.1963 (Rfree = 0.000) for 3135 atoms. Found 8 (18 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.1939 (Rfree = 0.000) for 3130 atoms. Found 8 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 3193 seeds are put forward NCS extension: 29 residues added (7 deleted due to clashes), 3222 seeds are put forward Round 1: 234 peptides, 33 chains. Longest chain 14 peptides. Score 0.538 Round 2: 253 peptides, 28 chains. Longest chain 21 peptides. Score 0.648 Round 3: 273 peptides, 32 chains. Longest chain 24 peptides. Score 0.652 Round 4: 288 peptides, 32 chains. Longest chain 29 peptides. Score 0.685 Round 5: 277 peptides, 28 chains. Longest chain 28 peptides. Score 0.701 Taking the results from Round 5 Chains 30, Residues 249, Estimated correctness of the model 58.1 % 2 chains (27 residues) have been docked in sequence Building loops using Loopy2018 30 chains (249 residues) following loop building 2 chains (27 residues) in sequence following loop building ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6747 restraints for refining 3164 atoms. 5640 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2290 (Rfree = 0.000) for 3164 atoms. Found 17 (18 requested) and removed 13 (11 requested) atoms. Cycle 22: After refmac, R = 0.2237 (Rfree = 0.000) for 3154 atoms. Found 12 (18 requested) and removed 15 (11 requested) atoms. Cycle 23: After refmac, R = 0.2145 (Rfree = 0.000) for 3147 atoms. Found 11 (17 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.2106 (Rfree = 0.000) for 3140 atoms. Found 11 (17 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.2017 (Rfree = 0.000) for 3130 atoms. Found 8 (17 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3213 seeds are put forward Round 1: 225 peptides, 31 chains. Longest chain 23 peptides. Score 0.538 Round 2: 263 peptides, 31 chains. Longest chain 24 peptides. Score 0.639 Round 3: 262 peptides, 31 chains. Longest chain 19 peptides. Score 0.637 Round 4: 264 peptides, 30 chains. Longest chain 33 peptides. Score 0.652 Round 5: 262 peptides, 33 chains. Longest chain 17 peptides. Score 0.614 Taking the results from Round 4 Chains 32, Residues 234, Estimated correctness of the model 44.7 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6592 restraints for refining 3164 atoms. 5493 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2333 (Rfree = 0.000) for 3164 atoms. Found 16 (16 requested) and removed 15 (11 requested) atoms. Cycle 27: After refmac, R = 0.2222 (Rfree = 0.000) for 3157 atoms. Found 16 (16 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2132 (Rfree = 0.000) for 3154 atoms. Found 8 (16 requested) and removed 18 (11 requested) atoms. Cycle 29: After refmac, R = 0.2043 (Rfree = 0.000) for 3140 atoms. Found 15 (16 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.2023 (Rfree = 0.000) for 3140 atoms. Found 8 (16 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 3220 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 3257 seeds are put forward Round 1: 216 peptides, 30 chains. Longest chain 16 peptides. Score 0.524 Round 2: 246 peptides, 28 chains. Longest chain 18 peptides. Score 0.631 Round 3: 243 peptides, 28 chains. Longest chain 24 peptides. Score 0.624 Round 4: 239 peptides, 29 chains. Longest chain 20 peptides. Score 0.602 Round 5: 241 peptides, 28 chains. Longest chain 17 peptides. Score 0.619 Taking the results from Round 2 Chains 31, Residues 218, Estimated correctness of the model 38.5 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6646 restraints for refining 3164 atoms. 5660 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2137 (Rfree = 0.000) for 3164 atoms. Found 9 (16 requested) and removed 13 (11 requested) atoms. Cycle 32: After refmac, R = 0.2114 (Rfree = 0.000) for 3149 atoms. Found 16 (16 requested) and removed 13 (11 requested) atoms. Cycle 33: After refmac, R = 0.2082 (Rfree = 0.000) for 3150 atoms. Found 16 (16 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.2036 (Rfree = 0.000) for 3146 atoms. Found 16 (16 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.2046 (Rfree = 0.000) for 3147 atoms. Found 16 (16 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 3231 seeds are put forward Round 1: 224 peptides, 34 chains. Longest chain 15 peptides. Score 0.495 Round 2: 243 peptides, 33 chains. Longest chain 15 peptides. Score 0.564 Round 3: 242 peptides, 29 chains. Longest chain 26 peptides. Score 0.609 Round 4: 229 peptides, 31 chains. Longest chain 21 peptides. Score 0.549 Round 5: 244 peptides, 31 chains. Longest chain 26 peptides. Score 0.591 Taking the results from Round 3 Chains 29, Residues 213, Estimated correctness of the model 31.6 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6754 restraints for refining 3164 atoms. 5809 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2260 (Rfree = 0.000) for 3164 atoms. Found 16 (16 requested) and removed 17 (11 requested) atoms. Cycle 37: After refmac, R = 0.2174 (Rfree = 0.000) for 3157 atoms. Found 16 (16 requested) and removed 15 (11 requested) atoms. Cycle 38: After refmac, R = 0.2181 (Rfree = 0.000) for 3156 atoms. Found 16 (16 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.2129 (Rfree = 0.000) for 3148 atoms. Found 16 (16 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.1793 (Rfree = 0.000) for 3148 atoms. Found 8 (16 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3235 seeds are put forward Round 1: 208 peptides, 35 chains. Longest chain 13 peptides. Score 0.428 Round 2: 228 peptides, 32 chains. Longest chain 17 peptides. Score 0.533 Round 3: 232 peptides, 31 chains. Longest chain 15 peptides. Score 0.558 Round 4: 236 peptides, 35 chains. Longest chain 10 peptides. Score 0.518 Round 5: 246 peptides, 36 chains. Longest chain 13 peptides. Score 0.534 Taking the results from Round 3 Chains 31, Residues 201, Estimated correctness of the model 14.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 7162 restraints for refining 3164 atoms. 6389 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2101 (Rfree = 0.000) for 3164 atoms. Found 16 (16 requested) and removed 14 (11 requested) atoms. Cycle 42: After refmac, R = 0.1989 (Rfree = 0.000) for 3163 atoms. Found 16 (16 requested) and removed 12 (11 requested) atoms. Cycle 43: After refmac, R = 0.1919 (Rfree = 0.000) for 3165 atoms. Found 16 (16 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1827 (Rfree = 0.000) for 3165 atoms. Found 16 (16 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1749 (Rfree = 0.000) for 3169 atoms. Found 13 (16 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3269 seeds are put forward Round 1: 190 peptides, 35 chains. Longest chain 11 peptides. Score 0.365 Round 2: 227 peptides, 34 chains. Longest chain 16 peptides. Score 0.504 Round 3: 224 peptides, 32 chains. Longest chain 16 peptides. Score 0.521 Round 4: 213 peptides, 30 chains. Longest chain 15 peptides. Score 0.515 Round 5: 217 peptides, 34 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 192, Estimated correctness of the model 0.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vmf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6666 reflections ( 99.72 % complete ) and 7276 restraints for refining 3164 atoms. 6540 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2050 (Rfree = 0.000) for 3164 atoms. Found 0 (16 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2025 (Rfree = 0.000) for 3151 atoms. Found 0 (16 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1994 (Rfree = 0.000) for 3139 atoms. Found 0 (16 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1946 (Rfree = 0.000) for 3126 atoms. TimeTaking 43.25