Mon 24 Dec 07:33:25 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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 07:33:29 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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 317 and 0 Target number of residues in the AU: 317 Target solvent content: 0.6226 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 62.30 5624 reflections ( 99.66 % complete ) and 0 restraints for refining 3871 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3068 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2828 (Rfree = 0.000) for 3871 atoms. Found 23 (24 requested) and removed 30 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 3920 seeds are put forward NCS extension: 0 residues added, 3920 seeds are put forward Round 1: 186 peptides, 33 chains. Longest chain 16 peptides. Score 0.382 Round 2: 233 peptides, 38 chains. Longest chain 22 peptides. Score 0.468 Round 3: 247 peptides, 30 chains. Longest chain 20 peptides. Score 0.611 Round 4: 260 peptides, 32 chains. Longest chain 31 peptides. Score 0.621 Round 5: 272 peptides, 30 chains. Longest chain 31 peptides. Score 0.671 Taking the results from Round 5 Chains 30, Residues 242, Estimated correctness of the model 40.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7003 restraints for refining 3154 atoms. 6065 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2513 (Rfree = 0.000) for 3154 atoms. Found 19 (20 requested) and removed 15 (10 requested) atoms. Cycle 2: After refmac, R = 0.2366 (Rfree = 0.000) for 3123 atoms. Found 17 (20 requested) and removed 19 (10 requested) atoms. Cycle 3: After refmac, R = 0.2311 (Rfree = 0.000) for 3108 atoms. Found 19 (20 requested) and removed 20 (10 requested) atoms. Cycle 4: After refmac, R = 0.2138 (Rfree = 0.000) for 3096 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 3085 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 3200 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3228 seeds are put forward Round 1: 234 peptides, 39 chains. Longest chain 14 peptides. Score 0.458 Round 2: 267 peptides, 36 chains. Longest chain 24 peptides. Score 0.593 Round 3: 264 peptides, 30 chains. Longest chain 22 peptides. Score 0.652 Round 4: 258 peptides, 31 chains. Longest chain 21 peptides. Score 0.627 Round 5: 252 peptides, 29 chains. Longest chain 23 peptides. Score 0.635 Taking the results from Round 3 Chains 31, Residues 234, Estimated correctness of the model 33.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 6958 restraints for refining 3154 atoms. 6012 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2213 (Rfree = 0.000) for 3154 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 7: After refmac, R = 0.2111 (Rfree = 0.000) for 3134 atoms. Found 12 (20 requested) and removed 16 (10 requested) atoms. Cycle 8: After refmac, R = 0.1960 (Rfree = 0.000) for 3122 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.1939 (Rfree = 0.000) for 3118 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.1660 (Rfree = 0.000) for 3115 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 3213 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3227 seeds are put forward Round 1: 216 peptides, 34 chains. Longest chain 22 peptides. Score 0.469 Round 2: 229 peptides, 35 chains. Longest chain 17 peptides. Score 0.496 Round 3: 251 peptides, 33 chains. Longest chain 20 peptides. Score 0.586 Round 4: 269 peptides, 35 chains. Longest chain 30 peptides. Score 0.609 Round 5: 253 peptides, 33 chains. Longest chain 21 peptides. Score 0.591 Taking the results from Round 4 Chains 36, Residues 234, Estimated correctness of the model 18.1 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 6901 restraints for refining 3154 atoms. 5947 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2013 (Rfree = 0.000) for 3154 atoms. Found 10 (20 requested) and removed 30 (10 requested) atoms. Cycle 12: After refmac, R = 0.1885 (Rfree = 0.000) for 3120 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. Cycle 13: After refmac, R = 0.1848 (Rfree = 0.000) for 3108 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.1657 (Rfree = 0.000) for 3099 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.1569 (Rfree = 0.000) for 3087 atoms. Found 1 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 3189 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3215 seeds are put forward Round 1: 222 peptides, 35 chains. Longest chain 14 peptides. Score 0.474 Round 2: 243 peptides, 34 chains. Longest chain 19 peptides. Score 0.551 Round 3: 246 peptides, 33 chains. Longest chain 21 peptides. Score 0.572 Round 4: 239 peptides, 30 chains. Longest chain 20 peptides. Score 0.590 Round 5: 253 peptides, 29 chains. Longest chain 20 peptides. Score 0.637 Taking the results from Round 5 Chains 29, Residues 224, Estimated correctness of the model 28.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7142 restraints for refining 3155 atoms. 6275 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2122 (Rfree = 0.000) for 3155 atoms. Found 12 (20 requested) and removed 22 (10 requested) atoms. Cycle 17: After refmac, R = 0.2199 (Rfree = 0.000) for 3134 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 18: After refmac, R = 0.2005 (Rfree = 0.000) for 3134 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. Cycle 19: After refmac, R = 0.1676 (Rfree = 0.000) for 3127 atoms. Found 3 (20 requested) and removed 13 (10 requested) atoms. Cycle 20: After refmac, R = 0.1736 (Rfree = 0.000) for 3112 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3243 seeds are put forward Round 1: 203 peptides, 37 chains. Longest chain 13 peptides. Score 0.381 Round 2: 221 peptides, 31 chains. Longest chain 18 peptides. Score 0.526 Round 3: 229 peptides, 34 chains. Longest chain 14 peptides. Score 0.510 Round 4: 224 peptides, 32 chains. Longest chain 17 peptides. Score 0.521 Round 5: 235 peptides, 30 chains. Longest chain 23 peptides. Score 0.579 Taking the results from Round 5 Chains 31, Residues 205, Estimated correctness of the model 6.3 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7090 restraints for refining 3155 atoms. 6230 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2095 (Rfree = 0.000) for 3155 atoms. Found 13 (20 requested) and removed 17 (10 requested) atoms. Cycle 22: After refmac, R = 0.1872 (Rfree = 0.000) for 3141 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.1782 (Rfree = 0.000) for 3133 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.1670 (Rfree = 0.000) for 3126 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.1619 (Rfree = 0.000) for 3114 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3213 seeds are put forward Round 1: 219 peptides, 37 chains. Longest chain 18 peptides. Score 0.436 Round 2: 234 peptides, 35 chains. Longest chain 20 peptides. Score 0.512 Round 3: 240 peptides, 38 chains. Longest chain 17 peptides. Score 0.490 Round 4: 240 peptides, 38 chains. Longest chain 13 peptides. Score 0.490 Round 5: 235 peptides, 33 chains. Longest chain 22 peptides. Score 0.541 Taking the results from Round 5 Chains 35, Residues 202, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7182 restraints for refining 3155 atoms. 6357 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2020 (Rfree = 0.000) for 3155 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.1987 (Rfree = 0.000) for 3144 atoms. Found 13 (20 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.1815 (Rfree = 0.000) for 3143 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1850 (Rfree = 0.000) for 3141 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1747 (Rfree = 0.000) for 3135 atoms. Found 10 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3249 seeds are put forward Round 1: 178 peptides, 33 chains. Longest chain 9 peptides. Score 0.352 Round 2: 207 peptides, 32 chains. Longest chain 20 peptides. Score 0.468 Round 3: 212 peptides, 34 chains. Longest chain 11 peptides. Score 0.456 Round 4: 214 peptides, 32 chains. Longest chain 16 peptides. Score 0.491 Round 5: 214 peptides, 29 chains. Longest chain 20 peptides. Score 0.532 Taking the results from Round 5 Chains 29, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7449 restraints for refining 3155 atoms. 6738 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2207 (Rfree = 0.000) for 3155 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 32: After refmac, R = 0.2043 (Rfree = 0.000) for 3150 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.1995 (Rfree = 0.000) for 3156 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.1684 (Rfree = 0.000) for 3160 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1743 (Rfree = 0.000) for 3155 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 3233 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3255 seeds are put forward Round 1: 179 peptides, 37 chains. Longest chain 9 peptides. Score 0.293 Round 2: 200 peptides, 34 chains. Longest chain 12 peptides. Score 0.416 Round 3: 204 peptides, 35 chains. Longest chain 12 peptides. Score 0.415 Round 4: 210 peptides, 30 chains. Longest chain 17 peptides. Score 0.506 Round 5: 203 peptides, 30 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 4 Chains 30, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7585 restraints for refining 3155 atoms. 6895 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1980 (Rfree = 0.000) for 3155 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. Cycle 37: After refmac, R = 0.1817 (Rfree = 0.000) for 3145 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.1779 (Rfree = 0.000) for 3138 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.1755 (Rfree = 0.000) for 3131 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.1522 (Rfree = 0.000) for 3127 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3194 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3212 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 10 peptides. Score 0.341 Round 2: 206 peptides, 32 chains. Longest chain 13 peptides. Score 0.465 Round 3: 208 peptides, 31 chains. Longest chain 17 peptides. Score 0.486 Round 4: 202 peptides, 28 chains. Longest chain 13 peptides. Score 0.509 Round 5: 198 peptides, 30 chains. Longest chain 13 peptides. Score 0.468 Taking the results from Round 4 Chains 28, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7395 restraints for refining 3155 atoms. 6727 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2030 (Rfree = 0.000) for 3155 atoms. Found 18 (20 requested) and removed 13 (10 requested) atoms. Cycle 42: After refmac, R = 0.1820 (Rfree = 0.000) for 3155 atoms. Found 15 (20 requested) and removed 15 (10 requested) atoms. Cycle 43: After refmac, R = 0.1850 (Rfree = 0.000) for 3153 atoms. Found 11 (20 requested) and removed 19 (10 requested) atoms. Cycle 44: After refmac, R = 0.1677 (Rfree = 0.000) for 3144 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1697 (Rfree = 0.000) for 3140 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 3207 seeds are put forward NCS extension: 0 residues added, 3207 seeds are put forward Round 1: 177 peptides, 34 chains. Longest chain 11 peptides. Score 0.333 Round 2: 187 peptides, 32 chains. Longest chain 11 peptides. Score 0.401 Round 3: 205 peptides, 34 chains. Longest chain 11 peptides. Score 0.433 Round 4: 211 peptides, 31 chains. Longest chain 12 peptides. Score 0.495 Round 5: 200 peptides, 32 chains. Longest chain 14 peptides. Score 0.445 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 180, 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 1vmf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5624 reflections ( 99.66 % complete ) and 7357 restraints for refining 3155 atoms. 6668 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2031 (Rfree = 0.000) for 3155 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1865 (Rfree = 0.000) for 3141 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1823 (Rfree = 0.000) for 3128 atoms. Found 0 (20 requested) and removed 3 (10 requested) atoms. Cycle 49: After refmac, R = 0.1823 (Rfree = 0.000) for 3123 atoms. TimeTaking 39.87