Mon 24 Dec 08:04:22 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmf-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-parrot-noncs ############### 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 08:04:27 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/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-parrot-noncs/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 335 and 0 Target number of residues in the AU: 335 Target solvent content: 0.6012 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-3.2-parrot-noncs.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-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 53.00 7960 reflections ( 99.76 % complete ) and 0 restraints for refining 3857 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3006 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2652 (Rfree = 0.000) for 3857 atoms. Found 31 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3930 seeds are put forward NCS extension: 0 residues added, 3930 seeds are put forward Round 1: 243 peptides, 37 chains. Longest chain 15 peptides. Score 0.513 Round 2: 282 peptides, 38 chains. Longest chain 18 peptides. Score 0.608 Round 3: 316 peptides, 38 chains. Longest chain 18 peptides. Score 0.687 Round 4: 319 peptides, 34 chains. Longest chain 20 peptides. Score 0.728 Round 5: 317 peptides, 30 chains. Longest chain 27 peptides. Score 0.758 Taking the results from Round 5 Chains 34, Residues 287, Estimated correctness of the model 76.5 % 2 chains (28 residues) have been docked in sequence Building loops using Loopy2018 34 chains (287 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6451 restraints for refining 3175 atoms. 5240 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2670 (Rfree = 0.000) for 3175 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 2: After refmac, R = 0.2509 (Rfree = 0.000) for 3140 atoms. Found 14 (27 requested) and removed 19 (14 requested) atoms. Cycle 3: After refmac, R = 0.2547 (Rfree = 0.000) for 3118 atoms. Found 19 (27 requested) and removed 18 (14 requested) atoms. Cycle 4: After refmac, R = 0.2549 (Rfree = 0.000) for 3102 atoms. Found 24 (25 requested) and removed 15 (13 requested) atoms. Cycle 5: After refmac, R = 0.2467 (Rfree = 0.000) for 3102 atoms. Found 21 (25 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3193 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3205 seeds are put forward Round 1: 264 peptides, 34 chains. Longest chain 19 peptides. Score 0.608 Round 2: 306 peptides, 30 chains. Longest chain 19 peptides. Score 0.739 Round 3: 325 peptides, 31 chains. Longest chain 27 peptides. Score 0.763 Round 4: 320 peptides, 32 chains. Longest chain 21 peptides. Score 0.747 Round 5: 323 peptides, 31 chains. Longest chain 27 peptides. Score 0.760 Taking the results from Round 3 Chains 33, Residues 294, Estimated correctness of the model 77.4 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6633 restraints for refining 3140 atoms. 5451 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2422 (Rfree = 0.000) for 3140 atoms. Found 25 (25 requested) and removed 22 (14 requested) atoms. Cycle 7: After refmac, R = 0.2249 (Rfree = 0.000) for 3140 atoms. Found 12 (25 requested) and removed 41 (14 requested) atoms. Cycle 8: After refmac, R = 0.2198 (Rfree = 0.000) for 3101 atoms. Found 14 (23 requested) and removed 28 (13 requested) atoms. Cycle 9: After refmac, R = 0.2127 (Rfree = 0.000) for 3085 atoms. Found 21 (23 requested) and removed 17 (13 requested) atoms. Cycle 10: After refmac, R = 0.2165 (Rfree = 0.000) for 3084 atoms. Found 13 (22 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 3.06 Search for helices and strands: 0 residues in 0 chains, 3182 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 3201 seeds are put forward Round 1: 290 peptides, 35 chains. Longest chain 18 peptides. Score 0.660 Round 2: 306 peptides, 31 chains. Longest chain 24 peptides. Score 0.730 Round 3: 335 peptides, 32 chains. Longest chain 22 peptides. Score 0.771 Round 4: 313 peptides, 32 chains. Longest chain 32 peptides. Score 0.734 Round 5: 303 peptides, 33 chains. Longest chain 27 peptides. Score 0.707 Taking the results from Round 3 Chains 35, Residues 303, Estimated correctness of the model 78.8 % 3 chains (45 residues) have been docked in sequence Building loops using Loopy2018 35 chains (303 residues) following loop building 3 chains (45 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6497 restraints for refining 3177 atoms. 5182 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2456 (Rfree = 0.000) for 3177 atoms. Found 22 (22 requested) and removed 18 (14 requested) atoms. Cycle 12: After refmac, R = 0.2367 (Rfree = 0.000) for 3174 atoms. Found 15 (22 requested) and removed 16 (14 requested) atoms. Cycle 13: After refmac, R = 0.2314 (Rfree = 0.000) for 3165 atoms. Found 18 (21 requested) and removed 15 (14 requested) atoms. Cycle 14: After refmac, R = 0.2713 (Rfree = 0.000) for 3163 atoms. Found 21 (21 requested) and removed 22 (14 requested) atoms. Cycle 15: After refmac, R = 0.2167 (Rfree = 0.000) for 3155 atoms. Found 12 (20 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3249 seeds are put forward NCS extension: 9 residues added (4 deleted due to clashes), 3258 seeds are put forward Round 1: 294 peptides, 35 chains. Longest chain 19 peptides. Score 0.669 Round 2: 312 peptides, 28 chains. Longest chain 35 peptides. Score 0.765 Round 3: 318 peptides, 28 chains. Longest chain 31 peptides. Score 0.775 Round 4: 310 peptides, 31 chains. Longest chain 28 peptides. Score 0.737 Round 5: 316 peptides, 31 chains. Longest chain 36 peptides. Score 0.748 Taking the results from Round 3 Chains 28, Residues 290, Estimated correctness of the model 79.4 % 3 chains (65 residues) have been docked in sequence Building loops using Loopy2018 28 chains (290 residues) following loop building 3 chains (65 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6320 restraints for refining 3177 atoms. 4941 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2454 (Rfree = 0.000) for 3177 atoms. Found 15 (20 requested) and removed 22 (14 requested) atoms. Cycle 17: After refmac, R = 0.2312 (Rfree = 0.000) for 3158 atoms. Found 11 (19 requested) and removed 17 (14 requested) atoms. Cycle 18: After refmac, R = 0.2292 (Rfree = 0.000) for 3148 atoms. Found 12 (18 requested) and removed 15 (14 requested) atoms. Cycle 19: After refmac, R = 0.2404 (Rfree = 0.000) for 3136 atoms. Found 18 (18 requested) and removed 15 (14 requested) atoms. Cycle 20: After refmac, R = 0.2262 (Rfree = 0.000) for 3130 atoms. Found 16 (17 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.98 3.06 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 3242 seeds are put forward Round 1: 280 peptides, 33 chains. Longest chain 24 peptides. Score 0.658 Round 2: 301 peptides, 30 chains. Longest chain 29 peptides. Score 0.730 Round 3: 299 peptides, 26 chains. Longest chain 29 peptides. Score 0.760 Round 4: 307 peptides, 32 chains. Longest chain 28 peptides. Score 0.723 Round 5: 318 peptides, 29 chains. Longest chain 27 peptides. Score 0.767 Taking the results from Round 5 Chains 31, Residues 289, Estimated correctness of the model 78.1 % 2 chains (37 residues) have been docked in sequence Building loops using Loopy2018 31 chains (289 residues) following loop building 2 chains (37 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6463 restraints for refining 3176 atoms. 5188 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2396 (Rfree = 0.000) for 3176 atoms. Found 17 (17 requested) and removed 17 (14 requested) atoms. Cycle 22: After refmac, R = 0.2304 (Rfree = 0.000) for 3165 atoms. Found 13 (16 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.2411 (Rfree = 0.000) for 3146 atoms. Found 16 (16 requested) and removed 20 (14 requested) atoms. Cycle 24: After refmac, R = 0.2398 (Rfree = 0.000) for 3137 atoms. Found 15 (15 requested) and removed 18 (14 requested) atoms. Cycle 25: After refmac, R = 0.2338 (Rfree = 0.000) for 3131 atoms. Found 15 (15 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3206 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3232 seeds are put forward Round 1: 276 peptides, 33 chains. Longest chain 22 peptides. Score 0.648 Round 2: 292 peptides, 28 chains. Longest chain 26 peptides. Score 0.730 Round 3: 293 peptides, 29 chains. Longest chain 27 peptides. Score 0.723 Round 4: 297 peptides, 32 chains. Longest chain 17 peptides. Score 0.704 Round 5: 289 peptides, 27 chains. Longest chain 26 peptides. Score 0.734 Taking the results from Round 5 Chains 28, Residues 262, Estimated correctness of the model 72.1 % 3 chains (60 residues) have been docked in sequence Building loops using Loopy2018 28 chains (262 residues) following loop building 3 chains (60 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6369 restraints for refining 3176 atoms. 5111 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2463 (Rfree = 0.000) for 3176 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 27: After refmac, R = 0.2314 (Rfree = 0.000) for 3164 atoms. Found 12 (14 requested) and removed 14 (14 requested) atoms. Cycle 28: After refmac, R = 0.2254 (Rfree = 0.000) for 3156 atoms. Found 7 (14 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.2207 (Rfree = 0.000) for 3147 atoms. Found 10 (14 requested) and removed 15 (14 requested) atoms. Cycle 30: After refmac, R = 0.2127 (Rfree = 0.000) for 3139 atoms. Found 11 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.96 3.04 Search for helices and strands: 0 residues in 0 chains, 3220 seeds are put forward NCS extension: 21 residues added (8 deleted due to clashes), 3241 seeds are put forward Round 1: 269 peptides, 37 chains. Longest chain 12 peptides. Score 0.586 Round 2: 288 peptides, 32 chains. Longest chain 18 peptides. Score 0.685 Round 3: 302 peptides, 33 chains. Longest chain 21 peptides. Score 0.705 Round 4: 292 peptides, 32 chains. Longest chain 20 peptides. Score 0.694 Round 5: 286 peptides, 30 chains. Longest chain 22 peptides. Score 0.700 Taking the results from Round 3 Chains 33, Residues 269, Estimated correctness of the model 66.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6942 restraints for refining 3177 atoms. 5899 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2301 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 32: After refmac, R = 0.2245 (Rfree = 0.000) for 3172 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 33: After refmac, R = 0.2157 (Rfree = 0.000) for 3169 atoms. Found 10 (14 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2126 (Rfree = 0.000) for 3163 atoms. Found 6 (14 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.2389 (Rfree = 0.000) for 3152 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3244 seeds are put forward Round 1: 259 peptides, 33 chains. Longest chain 16 peptides. Score 0.607 Round 2: 283 peptides, 32 chains. Longest chain 21 peptides. Score 0.675 Round 3: 278 peptides, 34 chains. Longest chain 21 peptides. Score 0.642 Round 4: 277 peptides, 32 chains. Longest chain 18 peptides. Score 0.661 Round 5: 283 peptides, 30 chains. Longest chain 21 peptides. Score 0.694 Taking the results from Round 5 Chains 30, Residues 253, Estimated correctness of the model 63.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6904 restraints for refining 3177 atoms. 5922 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2277 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 19 (14 requested) atoms. Cycle 37: After refmac, R = 0.2192 (Rfree = 0.000) for 3168 atoms. Found 12 (14 requested) and removed 18 (14 requested) atoms. Cycle 38: After refmac, R = 0.2183 (Rfree = 0.000) for 3161 atoms. Found 6 (14 requested) and removed 15 (14 requested) atoms. Cycle 39: After refmac, R = 0.2130 (Rfree = 0.000) for 3150 atoms. Found 8 (14 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.2153 (Rfree = 0.000) for 3141 atoms. Found 6 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 3.06 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 3233 seeds are put forward Round 1: 241 peptides, 30 chains. Longest chain 24 peptides. Score 0.595 Round 2: 261 peptides, 28 chains. Longest chain 25 peptides. Score 0.667 Round 3: 251 peptides, 28 chains. Longest chain 24 peptides. Score 0.643 Round 4: 280 peptides, 28 chains. Longest chain 30 peptides. Score 0.707 Round 5: 261 peptides, 28 chains. Longest chain 25 peptides. Score 0.667 Taking the results from Round 4 Chains 30, Residues 252, Estimated correctness of the model 66.7 % 2 chains (45 residues) have been docked in sequence Building loops using Loopy2018 30 chains (252 residues) following loop building 2 chains (45 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6255 restraints for refining 3177 atoms. 5042 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2401 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 27 (14 requested) atoms. Cycle 42: After refmac, R = 0.2232 (Rfree = 0.000) for 3160 atoms. Found 8 (14 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.2200 (Rfree = 0.000) for 3149 atoms. Found 5 (14 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.2257 (Rfree = 0.000) for 3138 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.2230 (Rfree = 0.000) for 3134 atoms. Found 8 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 3230 seeds are put forward Round 1: 229 peptides, 31 chains. Longest chain 17 peptides. Score 0.549 Round 2: 248 peptides, 28 chains. Longest chain 27 peptides. Score 0.636 Round 3: 248 peptides, 30 chains. Longest chain 18 peptides. Score 0.613 Round 4: 228 peptides, 26 chains. Longest chain 25 peptides. Score 0.609 Round 5: 233 peptides, 29 chains. Longest chain 20 peptides. Score 0.586 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 220, Estimated correctness of the model 50.4 % 1 chains (18 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vmf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7960 reflections ( 99.76 % complete ) and 6988 restraints for refining 3177 atoms. 6088 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2195 (Rfree = 0.000) for 3177 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2139 (Rfree = 0.000) for 3158 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2395 (Rfree = 0.000) for 3143 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2086 (Rfree = 0.000) for 3127 atoms. Found 0 (14 requested) and removed 11 (14 requested) atoms. Writing output files ... TimeTaking 39.35