Mon 24 Dec 00:34:01 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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 00:34:05 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.6-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 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-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-3.6-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 3.600 Wilson plot Bfac: 62.30 5624 reflections ( 99.66 % complete ) and 0 restraints for refining 3870 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3045 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2784 (Rfree = 0.000) for 3870 atoms. Found 22 (24 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 3937 seeds are put forward NCS extension: 0 residues added, 3937 seeds are put forward Round 1: 194 peptides, 38 chains. Longest chain 10 peptides. Score 0.333 Round 2: 259 peptides, 40 chains. Longest chain 12 peptides. Score 0.521 Round 3: 271 peptides, 38 chains. Longest chain 21 peptides. Score 0.580 Round 4: 294 peptides, 35 chains. Longest chain 22 peptides. Score 0.669 Round 5: 279 peptides, 35 chains. Longest chain 22 peptides. Score 0.634 Taking the results from Round 4 Chains 35, Residues 259, Estimated correctness of the model 39.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 6955 restraints for refining 3154 atoms. 5954 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2313 (Rfree = 0.000) for 3154 atoms. Found 18 (20 requested) and removed 19 (10 requested) atoms. Cycle 2: After refmac, R = 0.2066 (Rfree = 0.000) for 3110 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 3: After refmac, R = 0.2098 (Rfree = 0.000) for 3085 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 4: After refmac, R = 0.1960 (Rfree = 0.000) for 3072 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.1936 (Rfree = 0.000) for 3061 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 3170 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3199 seeds are put forward Round 1: 232 peptides, 38 chains. Longest chain 13 peptides. Score 0.465 Round 2: 248 peptides, 33 chains. Longest chain 26 peptides. Score 0.578 Round 3: 260 peptides, 34 chains. Longest chain 21 peptides. Score 0.598 Round 4: 262 peptides, 31 chains. Longest chain 27 peptides. Score 0.637 Round 5: 269 peptides, 31 chains. Longest chain 26 peptides. Score 0.653 Taking the results from Round 5 Chains 31, Residues 238, Estimated correctness of the model 34.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7030 restraints for refining 3154 atoms. 6109 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2324 (Rfree = 0.000) for 3154 atoms. Found 17 (20 requested) and removed 16 (10 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2319 (Rfree = 0.000) for 3127 atoms. Found 12 (20 requested) and removed 14 (10 requested) atoms. Cycle 8: After refmac, R = 0.1968 (Rfree = 0.000) for 3114 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. Cycle 9: After refmac, R = 0.1915 (Rfree = 0.000) for 3104 atoms. Found 1 (19 requested) and removed 13 (9 requested) atoms. Cycle 10: After refmac, R = 0.1901 (Rfree = 0.000) for 3089 atoms. Found 1 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.38 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: 216 peptides, 37 chains. Longest chain 16 peptides. Score 0.426 Round 2: 250 peptides, 36 chains. Longest chain 18 peptides. Score 0.546 Round 3: 255 peptides, 37 chains. Longest chain 25 peptides. Score 0.548 Round 4: 252 peptides, 33 chains. Longest chain 19 peptides. Score 0.588 Round 5: 255 peptides, 35 chains. Longest chain 28 peptides. Score 0.572 Taking the results from Round 4 Chains 33, Residues 219, Estimated correctness of the model 9.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7186 restraints for refining 3155 atoms. 6343 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2222 (Rfree = 0.000) for 3155 atoms. Found 20 (20 requested) and removed 56 (10 requested) atoms. Cycle 12: After refmac, R = 0.2109 (Rfree = 0.000) for 3107 atoms. Found 19 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.1983 (Rfree = 0.000) for 3096 atoms. Found 14 (19 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.1866 (Rfree = 0.000) for 3086 atoms. Found 11 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.1783 (Rfree = 0.000) for 3082 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 3181 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3212 seeds are put forward Round 1: 215 peptides, 38 chains. Longest chain 22 peptides. Score 0.408 Round 2: 246 peptides, 33 chains. Longest chain 23 peptides. Score 0.572 Round 3: 231 peptides, 31 chains. Longest chain 16 peptides. Score 0.555 Round 4: 245 peptides, 32 chains. Longest chain 23 peptides. Score 0.582 Round 5: 244 peptides, 34 chains. Longest chain 22 peptides. Score 0.554 Taking the results from Round 4 Chains 34, Residues 213, Estimated correctness of the model 7.5 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7048 restraints for refining 3155 atoms. 6143 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2125 (Rfree = 0.000) for 3155 atoms. Found 15 (20 requested) and removed 19 (10 requested) atoms. Cycle 17: After refmac, R = 0.1904 (Rfree = 0.000) for 3143 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.1815 (Rfree = 0.000) for 3130 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2159 (Rfree = 0.000) for 3122 atoms. Found 18 (20 requested) and removed 15 (10 requested) atoms. Cycle 20: After refmac, R = 0.2689 (Rfree = 0.000) for 3120 atoms. Found 20 (20 requested) and removed 54 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 3179 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3210 seeds are put forward Round 1: 186 peptides, 33 chains. Longest chain 18 peptides. Score 0.382 Round 2: 214 peptides, 30 chains. Longest chain 22 peptides. Score 0.518 Round 3: 222 peptides, 31 chains. Longest chain 26 peptides. Score 0.529 Round 4: 227 peptides, 34 chains. Longest chain 18 peptides. Score 0.504 Round 5: 222 peptides, 33 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 3 Chains 31, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7341 restraints for refining 3155 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2251 (Rfree = 0.000) for 3155 atoms. Found 20 (20 requested) and removed 36 (10 requested) atoms. Cycle 22: After refmac, R = 0.2061 (Rfree = 0.000) for 3123 atoms. Found 12 (20 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.1774 (Rfree = 0.000) for 3110 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.1686 (Rfree = 0.000) for 3097 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1645 (Rfree = 0.000) for 3086 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 3179 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3198 seeds are put forward Round 1: 201 peptides, 35 chains. Longest chain 19 peptides. Score 0.404 Round 2: 214 peptides, 34 chains. Longest chain 14 peptides. Score 0.463 Round 3: 212 peptides, 35 chains. Longest chain 16 peptides. Score 0.442 Round 4: 206 peptides, 29 chains. Longest chain 16 peptides. Score 0.507 Round 5: 210 peptides, 30 chains. Longest chain 20 peptides. Score 0.506 Taking the results from Round 4 Chains 29, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7411 restraints for refining 3155 atoms. 6732 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2192 (Rfree = 0.000) for 3155 atoms. Found 18 (20 requested) and removed 27 (10 requested) atoms. Cycle 27: After refmac, R = 0.1939 (Rfree = 0.000) for 3138 atoms. Found 10 (20 requested) and removed 20 (10 requested) atoms. Cycle 28: After refmac, R = 0.1857 (Rfree = 0.000) for 3126 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. Cycle 29: After refmac, R = 0.1807 (Rfree = 0.000) for 3118 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1724 (Rfree = 0.000) for 3111 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 3189 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3206 seeds are put forward Round 1: 193 peptides, 32 chains. Longest chain 14 peptides. Score 0.421 Round 2: 205 peptides, 33 chains. Longest chain 15 peptides. Score 0.447 Round 3: 213 peptides, 29 chains. Longest chain 19 peptides. Score 0.529 Round 4: 205 peptides, 29 chains. Longest chain 21 peptides. Score 0.504 Round 5: 204 peptides, 29 chains. Longest chain 12 peptides. Score 0.501 Taking the results from Round 3 Chains 29, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7381 restraints for refining 3154 atoms. 6674 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1860 (Rfree = 0.000) for 3154 atoms. Found 9 (20 requested) and removed 25 (10 requested) atoms. Cycle 32: After refmac, R = 0.1767 (Rfree = 0.000) for 3130 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. Cycle 33: After refmac, R = 0.1723 (Rfree = 0.000) for 3114 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.1670 (Rfree = 0.000) for 3116 atoms. Found 12 (19 requested) and removed 12 (9 requested) atoms. Cycle 35: After refmac, R = 0.1593 (Rfree = 0.000) for 3114 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 3199 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3217 seeds are put forward Round 1: 178 peptides, 35 chains. Longest chain 9 peptides. Score 0.321 Round 2: 196 peptides, 32 chains. Longest chain 16 peptides. Score 0.432 Round 3: 190 peptides, 31 chains. Longest chain 10 peptides. Score 0.426 Round 4: 195 peptides, 30 chains. Longest chain 15 peptides. Score 0.458 Round 5: 200 peptides, 31 chains. Longest chain 15 peptides. Score 0.460 Taking the results from Round 5 Chains 31, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7382 restraints for refining 3155 atoms. 6737 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1924 (Rfree = 0.000) for 3155 atoms. Found 15 (20 requested) and removed 16 (10 requested) atoms. Cycle 37: After refmac, R = 0.1794 (Rfree = 0.000) for 3141 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 3131 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.1671 (Rfree = 0.000) for 3128 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1671 (Rfree = 0.000) for 3118 atoms. Found 3 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 3174 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3190 seeds are put forward Round 1: 162 peptides, 32 chains. Longest chain 12 peptides. Score 0.308 Round 2: 208 peptides, 35 chains. Longest chain 16 peptides. Score 0.428 Round 3: 192 peptides, 31 chains. Longest chain 15 peptides. Score 0.433 Round 4: 189 peptides, 28 chains. Longest chain 15 peptides. Score 0.467 Round 5: 201 peptides, 30 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 5 Chains 30, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.66 % complete ) and 7381 restraints for refining 3155 atoms. 6727 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1949 (Rfree = 0.000) for 3155 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.1824 (Rfree = 0.000) for 3141 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.1848 (Rfree = 0.000) for 3128 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1797 (Rfree = 0.000) for 3127 atoms. Found 10 (20 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.1764 (Rfree = 0.000) for 3123 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 3209 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 163 peptides, 34 chains. Longest chain 9 peptides. Score 0.279 Round 2: 192 peptides, 32 chains. Longest chain 14 peptides. Score 0.418 Round 3: 211 peptides, 33 chains. Longest chain 12 peptides. Score 0.467 Round 4: 202 peptides, 33 chains. Longest chain 13 peptides. Score 0.437 Round 5: 218 peptides, 31 chains. Longest chain 15 peptides. Score 0.517 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 187, 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 7134 restraints for refining 3155 atoms. 6417 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1969 (Rfree = 0.000) for 3155 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1901 (Rfree = 0.000) for 3143 atoms. Found 0 (20 requested) and removed 7 (10 requested) atoms. Cycle 48: After refmac, R = 0.1867 (Rfree = 0.000) for 3133 atoms. Found 0 (20 requested) and removed 5 (10 requested) atoms. Cycle 49: After refmac, R = 0.1863 (Rfree = 0.000) for 3127 atoms. TimeTaking 38.07