Mon 24 Dec 00:23:22 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 1vlm-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-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/1vlm-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-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 00:23:27 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-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 307 and 0 Target number of residues in the AU: 307 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.70 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: 93.922 3.400 Wilson plot Bfac: 60.57 6393 reflections ( 99.72 % complete ) and 0 restraints for refining 3858 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3099 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2702 (Rfree = 0.000) for 3858 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3917 seeds are put forward NCS extension: 0 residues added, 3917 seeds are put forward Round 1: 203 peptides, 39 chains. Longest chain 10 peptides. Score 0.357 Round 2: 255 peptides, 34 chains. Longest chain 25 peptides. Score 0.596 Round 3: 258 peptides, 31 chains. Longest chain 32 peptides. Score 0.639 Round 4: 266 peptides, 28 chains. Longest chain 30 peptides. Score 0.690 Round 5: 272 peptides, 36 chains. Longest chain 26 peptides. Score 0.617 Taking the results from Round 4 Chains 31, Residues 238, Estimated correctness of the model 55.3 % 3 chains (65 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 6414 restraints for refining 3186 atoms. 5237 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2461 (Rfree = 0.000) for 3186 atoms. Found 17 (24 requested) and removed 34 (12 requested) atoms. Cycle 2: After refmac, R = 0.2352 (Rfree = 0.000) for 3137 atoms. Found 11 (23 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2311 (Rfree = 0.000) for 3115 atoms. Found 5 (23 requested) and removed 15 (11 requested) atoms. Cycle 4: After refmac, R = 0.2188 (Rfree = 0.000) for 3092 atoms. Found 5 (23 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2152 (Rfree = 0.000) for 3074 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 3170 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 3184 seeds are put forward Round 1: 240 peptides, 34 chains. Longest chain 17 peptides. Score 0.553 Round 2: 281 peptides, 30 chains. Longest chain 29 peptides. Score 0.702 Round 3: 265 peptides, 36 chains. Longest chain 15 peptides. Score 0.599 Round 4: 278 peptides, 32 chains. Longest chain 35 peptides. Score 0.676 Round 5: 291 peptides, 29 chains. Longest chain 39 peptides. Score 0.732 Taking the results from Round 5 Chains 30, Residues 262, Estimated correctness of the model 65.7 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 6713 restraints for refining 3185 atoms. 5587 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2384 (Rfree = 0.000) for 3185 atoms. Found 23 (24 requested) and removed 46 (12 requested) atoms. Cycle 7: After refmac, R = 0.2209 (Rfree = 0.000) for 3151 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. Cycle 8: After refmac, R = 0.2105 (Rfree = 0.000) for 3138 atoms. Found 15 (22 requested) and removed 22 (11 requested) atoms. Cycle 9: After refmac, R = 0.2010 (Rfree = 0.000) for 3125 atoms. Found 4 (22 requested) and removed 19 (11 requested) atoms. Cycle 10: After refmac, R = 0.1926 (Rfree = 0.000) for 3104 atoms. Found 3 (21 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.40 Search for helices and strands: 0 residues in 0 chains, 3173 seeds are put forward NCS extension: 35 residues added (6 deleted due to clashes), 3208 seeds are put forward Round 1: 251 peptides, 38 chains. Longest chain 22 peptides. Score 0.534 Round 2: 256 peptides, 36 chains. Longest chain 19 peptides. Score 0.574 Round 3: 271 peptides, 35 chains. Longest chain 24 peptides. Score 0.626 Round 4: 263 peptides, 34 chains. Longest chain 17 peptides. Score 0.617 Round 5: 268 peptides, 32 chains. Longest chain 22 peptides. Score 0.652 Taking the results from Round 5 Chains 32, Residues 236, Estimated correctness of the model 44.7 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 6774 restraints for refining 3185 atoms. 5720 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2588 (Rfree = 0.000) for 3185 atoms. Found 15 (22 requested) and removed 33 (12 requested) atoms. Cycle 12: After refmac, R = 0.2334 (Rfree = 0.000) for 3152 atoms. Found 8 (21 requested) and removed 19 (11 requested) atoms. Cycle 13: After refmac, R = 0.2218 (Rfree = 0.000) for 3136 atoms. Found 11 (21 requested) and removed 13 (11 requested) atoms. Cycle 14: After refmac, R = 0.2129 (Rfree = 0.000) for 3133 atoms. Found 4 (21 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.2072 (Rfree = 0.000) for 3124 atoms. Found 2 (21 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3234 seeds are put forward Round 1: 231 peptides, 36 chains. Longest chain 13 peptides. Score 0.499 Round 2: 268 peptides, 36 chains. Longest chain 23 peptides. Score 0.607 Round 3: 263 peptides, 34 chains. Longest chain 20 peptides. Score 0.617 Round 4: 266 peptides, 37 chains. Longest chain 19 peptides. Score 0.590 Round 5: 244 peptides, 32 chains. Longest chain 37 peptides. Score 0.590 Taking the results from Round 3 Chains 34, Residues 229, Estimated correctness of the model 34.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7224 restraints for refining 3186 atoms. 6342 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2290 (Rfree = 0.000) for 3186 atoms. Found 20 (22 requested) and removed 26 (12 requested) atoms. Cycle 17: After refmac, R = 0.2109 (Rfree = 0.000) for 3169 atoms. Found 10 (22 requested) and removed 19 (12 requested) atoms. Cycle 18: After refmac, R = 0.2024 (Rfree = 0.000) for 3155 atoms. Found 9 (21 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.1937 (Rfree = 0.000) for 3145 atoms. Found 3 (21 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1927 (Rfree = 0.000) for 3133 atoms. Found 3 (21 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.44 Search for helices and strands: 0 residues in 0 chains, 3227 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3247 seeds are put forward Round 1: 205 peptides, 31 chains. Longest chain 19 peptides. Score 0.485 Round 2: 218 peptides, 27 chains. Longest chain 17 peptides. Score 0.580 Round 3: 223 peptides, 30 chains. Longest chain 24 peptides. Score 0.556 Round 4: 240 peptides, 32 chains. Longest chain 22 peptides. Score 0.579 Round 5: 250 peptides, 29 chains. Longest chain 15 peptides. Score 0.642 Taking the results from Round 5 Chains 29, Residues 221, Estimated correctness of the model 41.8 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7081 restraints for refining 3186 atoms. 6203 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2364 (Rfree = 0.000) for 3186 atoms. Found 22 (22 requested) and removed 18 (12 requested) atoms. Cycle 22: After refmac, R = 0.2183 (Rfree = 0.000) for 3182 atoms. Found 22 (22 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.2152 (Rfree = 0.000) for 3171 atoms. Found 17 (22 requested) and removed 14 (12 requested) atoms. Cycle 24: After refmac, R = 0.2089 (Rfree = 0.000) for 3166 atoms. Found 11 (21 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.2072 (Rfree = 0.000) for 3155 atoms. Found 13 (21 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3257 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3269 seeds are put forward Round 1: 198 peptides, 35 chains. Longest chain 12 peptides. Score 0.401 Round 2: 225 peptides, 30 chains. Longest chain 15 peptides. Score 0.561 Round 3: 215 peptides, 30 chains. Longest chain 13 peptides. Score 0.531 Round 4: 234 peptides, 32 chains. Longest chain 14 peptides. Score 0.562 Round 5: 235 peptides, 32 chains. Longest chain 18 peptides. Score 0.565 Taking the results from Round 5 Chains 33, Residues 203, Estimated correctness of the model 16.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7216 restraints for refining 3185 atoms. 6397 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2192 (Rfree = 0.000) for 3185 atoms. Found 22 (22 requested) and removed 28 (12 requested) atoms. Cycle 27: After refmac, R = 0.2101 (Rfree = 0.000) for 3174 atoms. Found 11 (21 requested) and removed 16 (11 requested) atoms. Cycle 28: After refmac, R = 0.2029 (Rfree = 0.000) for 3165 atoms. Found 10 (21 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.2047 (Rfree = 0.000) for 3158 atoms. Found 20 (21 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1996 (Rfree = 0.000) for 3162 atoms. Found 8 (21 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.43 Search for helices and strands: 0 residues in 0 chains, 3252 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3271 seeds are put forward Round 1: 174 peptides, 32 chains. Longest chain 11 peptides. Score 0.359 Round 2: 205 peptides, 31 chains. Longest chain 12 peptides. Score 0.485 Round 3: 231 peptides, 37 chains. Longest chain 13 peptides. Score 0.485 Round 4: 235 peptides, 32 chains. Longest chain 14 peptides. Score 0.565 Round 5: 226 peptides, 31 chains. Longest chain 14 peptides. Score 0.551 Taking the results from Round 4 Chains 32, Residues 203, Estimated correctness of the model 16.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7188 restraints for refining 3186 atoms. 6408 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2143 (Rfree = 0.000) for 3186 atoms. Found 21 (22 requested) and removed 14 (12 requested) atoms. Cycle 32: After refmac, R = 0.2060 (Rfree = 0.000) for 3183 atoms. Found 9 (22 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.1994 (Rfree = 0.000) for 3174 atoms. Found 7 (21 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.1904 (Rfree = 0.000) for 3164 atoms. Found 3 (21 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1862 (Rfree = 0.000) for 3155 atoms. Found 2 (21 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3244 seeds are put forward Round 1: 177 peptides, 31 chains. Longest chain 13 peptides. Score 0.387 Round 2: 204 peptides, 30 chains. Longest chain 14 peptides. Score 0.496 Round 3: 206 peptides, 29 chains. Longest chain 15 peptides. Score 0.517 Round 4: 206 peptides, 30 chains. Longest chain 14 peptides. Score 0.503 Round 5: 198 peptides, 33 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 3 Chains 29, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7391 restraints for refining 3174 atoms. 6712 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2036 (Rfree = 0.000) for 3174 atoms. Found 21 (21 requested) and removed 14 (11 requested) atoms. Cycle 37: After refmac, R = 0.1932 (Rfree = 0.000) for 3179 atoms. Found 9 (22 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1861 (Rfree = 0.000) for 3174 atoms. Found 7 (21 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1807 (Rfree = 0.000) for 3170 atoms. Found 1 (21 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1790 (Rfree = 0.000) for 3157 atoms. Found 2 (21 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.43 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3240 seeds are put forward Round 1: 176 peptides, 29 chains. Longest chain 15 peptides. Score 0.415 Round 2: 192 peptides, 28 chains. Longest chain 17 peptides. Score 0.486 Round 3: 186 peptides, 26 chains. Longest chain 15 peptides. Score 0.496 Round 4: 192 peptides, 26 chains. Longest chain 18 peptides. Score 0.515 Round 5: 191 peptides, 27 chains. Longest chain 16 peptides. Score 0.497 Taking the results from Round 4 Chains 26, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7492 restraints for refining 3179 atoms. 6854 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2015 (Rfree = 0.000) for 3179 atoms. Found 11 (22 requested) and removed 24 (12 requested) atoms. Cycle 42: After refmac, R = 0.1919 (Rfree = 0.000) for 3163 atoms. Found 20 (21 requested) and removed 13 (11 requested) atoms. Cycle 43: After refmac, R = 0.1830 (Rfree = 0.000) for 3168 atoms. Found 6 (21 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1815 (Rfree = 0.000) for 3160 atoms. Found 2 (21 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1903 (Rfree = 0.000) for 3151 atoms. Found 10 (21 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 3246 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3267 seeds are put forward Round 1: 167 peptides, 30 chains. Longest chain 9 peptides. Score 0.365 Round 2: 175 peptides, 27 chains. Longest chain 14 peptides. Score 0.443 Round 3: 169 peptides, 26 chains. Longest chain 14 peptides. Score 0.437 Round 4: 171 peptides, 24 chains. Longest chain 14 peptides. Score 0.475 Round 5: 167 peptides, 23 chains. Longest chain 14 peptides. Score 0.477 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 144, 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 1vlm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6393 reflections ( 99.72 % complete ) and 7577 restraints for refining 3185 atoms. 7024 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1958 (Rfree = 0.000) for 3185 atoms. Found 0 (22 requested) and removed 9 (12 requested) atoms. Cycle 47: After refmac, R = 0.1989 (Rfree = 0.000) for 3174 atoms. Found 0 (21 requested) and removed 2 (11 requested) atoms. Cycle 48: After refmac, R = 0.1918 (Rfree = 0.000) for 3172 atoms. Found 0 (21 requested) and removed 1 (11 requested) atoms. Cycle 49: After refmac, R = 0.1666 (Rfree = 0.000) for 3170 atoms. TimeTaking 36.5