null Mon 24 Dec 07:39:55 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 1vlm-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.4-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/1vlm-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.4-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 07:40:00 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/1vlm-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.4-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 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-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3504 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: 93.922 3.400 Wilson plot Bfac: 60.57 6393 reflections ( 99.72 % complete ) and 0 restraints for refining 3912 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3159 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2877 (Rfree = 0.000) for 3912 atoms. Found 29 (29 requested) and removed 111 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3907 seeds are put forward NCS extension: 0 residues added, 3907 seeds are put forward Round 1: 172 peptides, 35 chains. Longest chain 11 peptides. Score 0.302 Round 2: 236 peptides, 38 chains. Longest chain 22 peptides. Score 0.487 Round 3: 265 peptides, 39 chains. Longest chain 28 peptides. Score 0.562 Round 4: 262 peptides, 42 chains. Longest chain 21 peptides. Score 0.515 Round 5: 270 peptides, 35 chains. Longest chain 17 peptides. Score 0.624 Taking the results from Round 5 Chains 36, Residues 235, Estimated correctness of the model 36.3 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7066 restraints for refining 3185 atoms. 6122 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2643 (Rfree = 0.000) for 3185 atoms. Found 18 (24 requested) and removed 35 (12 requested) atoms. Cycle 2: After refmac, R = 0.2422 (Rfree = 0.000) for 3142 atoms. Found 6 (23 requested) and removed 28 (11 requested) atoms. Cycle 3: After refmac, R = 0.2329 (Rfree = 0.000) for 3103 atoms. Found 7 (23 requested) and removed 23 (11 requested) atoms. Cycle 4: After refmac, R = 0.2224 (Rfree = 0.000) for 3082 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. Cycle 5: After refmac, R = 0.2162 (Rfree = 0.000) for 3064 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3177 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3192 seeds are put forward Round 1: 227 peptides, 32 chains. Longest chain 23 peptides. Score 0.541 Round 2: 255 peptides, 29 chains. Longest chain 28 peptides. Score 0.654 Round 3: 247 peptides, 28 chains. Longest chain 28 peptides. Score 0.646 Round 4: 252 peptides, 29 chains. Longest chain 30 peptides. Score 0.647 Round 5: 250 peptides, 29 chains. Longest chain 26 peptides. Score 0.642 Taking the results from Round 2 Chains 31, Residues 226, Estimated correctness of the model 45.3 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 6583 restraints for refining 3185 atoms. 5523 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2345 (Rfree = 0.000) for 3185 atoms. Found 15 (24 requested) and removed 23 (12 requested) atoms. Cycle 7: After refmac, R = 0.2225 (Rfree = 0.000) for 3163 atoms. Found 14 (23 requested) and removed 17 (11 requested) atoms. Cycle 8: After refmac, R = 0.2123 (Rfree = 0.000) for 3158 atoms. Found 9 (23 requested) and removed 12 (11 requested) atoms. Cycle 9: After refmac, R = 0.2102 (Rfree = 0.000) for 3152 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.2006 (Rfree = 0.000) for 3136 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 3196 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3219 seeds are put forward Round 1: 240 peptides, 37 chains. Longest chain 21 peptides. Score 0.514 Round 2: 265 peptides, 33 chains. Longest chain 26 peptides. Score 0.634 Round 3: 259 peptides, 31 chains. Longest chain 26 peptides. Score 0.641 Round 4: 258 peptides, 31 chains. Longest chain 29 peptides. Score 0.639 Round 5: 263 peptides, 33 chains. Longest chain 28 peptides. Score 0.629 Taking the results from Round 3 Chains 31, Residues 228, Estimated correctness of the model 41.5 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 6689 restraints for refining 3186 atoms. 5660 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2394 (Rfree = 0.000) for 3186 atoms. Found 18 (24 requested) and removed 22 (12 requested) atoms. Cycle 12: After refmac, R = 0.2252 (Rfree = 0.000) for 3170 atoms. Found 6 (24 requested) and removed 22 (12 requested) atoms. Cycle 13: After refmac, R = 0.2276 (Rfree = 0.000) for 3148 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.2211 (Rfree = 0.000) for 3130 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.2192 (Rfree = 0.000) for 3117 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.43 Search for helices and strands: 0 residues in 0 chains, 3193 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 3227 seeds are put forward Round 1: 213 peptides, 32 chains. Longest chain 26 peptides. Score 0.497 Round 2: 244 peptides, 32 chains. Longest chain 24 peptides. Score 0.590 Round 3: 246 peptides, 31 chains. Longest chain 25 peptides. Score 0.608 Round 4: 229 peptides, 26 chains. Longest chain 26 peptides. Score 0.623 Round 5: 230 peptides, 29 chains. Longest chain 26 peptides. Score 0.589 Taking the results from Round 4 Chains 29, Residues 203, Estimated correctness of the model 36.0 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 6555 restraints for refining 3185 atoms. 5522 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2424 (Rfree = 0.000) for 3185 atoms. Found 13 (24 requested) and removed 23 (12 requested) atoms. Cycle 17: After refmac, R = 0.2310 (Rfree = 0.000) for 3154 atoms. Found 6 (23 requested) and removed 18 (11 requested) atoms. Cycle 18: After refmac, R = 0.2298 (Rfree = 0.000) for 3129 atoms. Found 20 (23 requested) and removed 16 (11 requested) atoms. Cycle 19: After refmac, R = 0.2140 (Rfree = 0.000) for 3130 atoms. Found 5 (23 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.2159 (Rfree = 0.000) for 3114 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 3205 seeds are put forward NCS extension: 10 residues added (10 deleted due to clashes), 3215 seeds are put forward Round 1: 198 peptides, 31 chains. Longest chain 12 peptides. Score 0.462 Round 2: 227 peptides, 29 chains. Longest chain 18 peptides. Score 0.580 Round 3: 228 peptides, 31 chains. Longest chain 24 peptides. Score 0.557 Round 4: 214 peptides, 27 chains. Longest chain 17 peptides. Score 0.569 Round 5: 239 peptides, 30 chains. Longest chain 19 peptides. Score 0.601 Taking the results from Round 5 Chains 31, Residues 209, Estimated correctness of the model 29.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7191 restraints for refining 3186 atoms. 6336 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2374 (Rfree = 0.000) for 3186 atoms. Found 12 (24 requested) and removed 26 (12 requested) atoms. Cycle 22: After refmac, R = 0.2301 (Rfree = 0.000) for 3163 atoms. Found 13 (23 requested) and removed 19 (11 requested) atoms. Cycle 23: After refmac, R = 0.2153 (Rfree = 0.000) for 3150 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 24: After refmac, R = 0.2023 (Rfree = 0.000) for 3138 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.1997 (Rfree = 0.000) for 3125 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 3223 seeds are put forward NCS extension: 10 residues added (7 deleted due to clashes), 3233 seeds are put forward Round 1: 224 peptides, 36 chains. Longest chain 16 peptides. Score 0.476 Round 2: 227 peptides, 30 chains. Longest chain 17 peptides. Score 0.567 Round 3: 239 peptides, 34 chains. Longest chain 25 peptides. Score 0.550 Round 4: 240 peptides, 35 chains. Longest chain 16 peptides. Score 0.540 Round 5: 242 peptides, 34 chains. Longest chain 24 peptides. Score 0.559 Taking the results from Round 2 Chains 30, Residues 197, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7266 restraints for refining 3176 atoms. 6508 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2276 (Rfree = 0.000) for 3176 atoms. Found 17 (23 requested) and removed 11 (11 requested) atoms. Cycle 27: After refmac, R = 0.2137 (Rfree = 0.000) for 3179 atoms. Found 12 (24 requested) and removed 16 (12 requested) atoms. Cycle 28: After refmac, R = 0.2009 (Rfree = 0.000) for 3171 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.1964 (Rfree = 0.000) for 3159 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1943 (Rfree = 0.000) for 3147 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 3241 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 3262 seeds are put forward Round 1: 204 peptides, 34 chains. Longest chain 12 peptides. Score 0.438 Round 2: 224 peptides, 31 chains. Longest chain 20 peptides. Score 0.545 Round 3: 220 peptides, 31 chains. Longest chain 16 peptides. Score 0.533 Round 4: 228 peptides, 30 chains. Longest chain 24 peptides. Score 0.570 Round 5: 235 peptides, 33 chains. Longest chain 16 peptides. Score 0.552 Taking the results from Round 4 Chains 30, Residues 198, Estimated correctness of the model 18.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7247 restraints for refining 3186 atoms. 6485 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2167 (Rfree = 0.000) for 3186 atoms. Found 12 (24 requested) and removed 15 (12 requested) atoms. Cycle 32: After refmac, R = 0.1988 (Rfree = 0.000) for 3174 atoms. Found 6 (24 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.1892 (Rfree = 0.000) for 3158 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1798 (Rfree = 0.000) for 3151 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1795 (Rfree = 0.000) for 3146 atoms. Found 9 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.38 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3251 seeds are put forward Round 1: 199 peptides, 32 chains. Longest chain 25 peptides. Score 0.450 Round 2: 205 peptides, 28 chains. Longest chain 25 peptides. Score 0.528 Round 3: 225 peptides, 32 chains. Longest chain 17 peptides. Score 0.535 Round 4: 229 peptides, 33 chains. Longest chain 22 peptides. Score 0.534 Round 5: 237 peptides, 36 chains. Longest chain 26 peptides. Score 0.518 Taking the results from Round 3 Chains 33, Residues 193, Estimated correctness of the model 6.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7088 restraints for refining 3185 atoms. 6251 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1982 (Rfree = 0.000) for 3185 atoms. Found 14 (24 requested) and removed 14 (12 requested) atoms. Cycle 37: After refmac, R = 0.1870 (Rfree = 0.000) for 3179 atoms. Found 7 (24 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.1878 (Rfree = 0.000) for 3169 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. Cycle 39: After refmac, R = 0.1744 (Rfree = 0.000) for 3162 atoms. Found 10 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1687 (Rfree = 0.000) for 3157 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.36 Search for helices and strands: 0 residues in 0 chains, 3227 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3240 seeds are put forward Round 1: 190 peptides, 36 chains. Longest chain 10 peptides. Score 0.356 Round 2: 204 peptides, 32 chains. Longest chain 13 peptides. Score 0.467 Round 3: 221 peptides, 34 chains. Longest chain 19 peptides. Score 0.495 Round 4: 222 peptides, 34 chains. Longest chain 17 peptides. Score 0.498 Round 5: 219 peptides, 36 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 4 Chains 34, Residues 188, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6393 reflections ( 99.72 % complete ) and 7346 restraints for refining 3186 atoms. 6586 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2165 (Rfree = 0.000) for 3186 atoms. Found 12 (24 requested) and removed 19 (12 requested) atoms. Cycle 42: After refmac, R = 0.2053 (Rfree = 0.000) for 3170 atoms. Found 13 (24 requested) and removed 15 (12 requested) atoms. Cycle 43: After refmac, R = 0.1902 (Rfree = 0.000) for 3153 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1837 (Rfree = 0.000) for 3143 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.1774 (Rfree = 0.000) for 3131 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.38 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3209 seeds are put forward Round 1: 157 peptides, 29 chains. Longest chain 12 peptides. Score 0.343 Round 2: 197 peptides, 32 chains. Longest chain 14 peptides. Score 0.443 Round 3: 205 peptides, 31 chains. Longest chain 12 peptides. Score 0.485 Round 4: 202 peptides, 30 chains. Longest chain 13 peptides. Score 0.490 Round 5: 205 peptides, 31 chains. Longest chain 13 peptides. Score 0.485 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 172, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 4 % 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 7305 restraints for refining 3186 atoms. 6625 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1981 (Rfree = 0.000) for 3186 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1814 (Rfree = 0.000) for 3169 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1772 (Rfree = 0.000) for 3154 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1725 (Rfree = 0.000) for 3138 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:19:05 GMT 2018 Job finished. TimeTaking 39.17 Used memory is bytes: 19320056