Mon 24 Dec 01:02:02 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 1vjn-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-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/1vjn-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-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 01:02:07 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/1vjn-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-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 381 and 0 Target number of residues in the AU: 381 Target solvent content: 0.5209 Checking the provided sequence file Detected sequence length: 220 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 440 Adjusted target solvent content: 0.45 Input MTZ file: 1vjn-3.2-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: 1 Cell parameters: 43.059 45.719 63.384 73.681 89.271 64.860 Input sequence file: 1vjn-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.60 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: 60.370 3.200 Wilson plot Bfac: 28.02 6759 reflections ( 98.21 % complete ) and 0 restraints for refining 3913 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.2840 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2274 (Rfree = 0.000) for 3913 atoms. Found 35 (35 requested) and removed 32 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.70 2.89 Search for helices and strands: 0 residues in 0 chains, 3973 seeds are put forward NCS extension: 0 residues added, 3973 seeds are put forward Round 1: 200 peptides, 41 chains. Longest chain 8 peptides. Score 0.315 Round 2: 239 peptides, 39 chains. Longest chain 12 peptides. Score 0.486 Round 3: 257 peptides, 39 chains. Longest chain 13 peptides. Score 0.543 Round 4: 275 peptides, 37 chains. Longest chain 16 peptides. Score 0.618 Round 5: 278 peptides, 36 chains. Longest chain 17 peptides. Score 0.637 Taking the results from Round 5 Chains 36, Residues 242, Estimated correctness of the model 50.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6971 restraints for refining 3211 atoms. 6020 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2286 (Rfree = 0.000) for 3211 atoms. Found 26 (28 requested) and removed 27 (14 requested) atoms. Cycle 2: After refmac, R = 0.2137 (Rfree = 0.000) for 3182 atoms. Found 10 (28 requested) and removed 16 (14 requested) atoms. Cycle 3: After refmac, R = 0.2058 (Rfree = 0.000) for 3163 atoms. Found 11 (28 requested) and removed 16 (14 requested) atoms. Cycle 4: After refmac, R = 0.2016 (Rfree = 0.000) for 3145 atoms. Found 11 (28 requested) and removed 15 (14 requested) atoms. Cycle 5: After refmac, R = 0.1981 (Rfree = 0.000) for 3136 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.60 2.78 Search for helices and strands: 0 residues in 0 chains, 3213 seeds are put forward NCS extension: 25 residues added (9 deleted due to clashes), 3238 seeds are put forward Round 1: 247 peptides, 37 chains. Longest chain 14 peptides. Score 0.539 Round 2: 285 peptides, 32 chains. Longest chain 25 peptides. Score 0.696 Round 3: 296 peptides, 35 chains. Longest chain 27 peptides. Score 0.690 Round 4: 288 peptides, 30 chains. Longest chain 23 peptides. Score 0.721 Round 5: 308 peptides, 32 chains. Longest chain 26 peptides. Score 0.742 Taking the results from Round 5 Chains 34, Residues 276, Estimated correctness of the model 73.6 % 3 chains (58 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 189 A 33 chains (282 residues) following loop building 2 chains (68 residues) in sequence following loop building ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6045 restraints for refining 3213 atoms. 4683 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2495 (Rfree = 0.000) for 3213 atoms. Found 27 (28 requested) and removed 27 (14 requested) atoms. Cycle 7: After refmac, R = 0.2260 (Rfree = 0.000) for 3193 atoms. Found 13 (27 requested) and removed 22 (14 requested) atoms. Cycle 8: After refmac, R = 0.2242 (Rfree = 0.000) for 3172 atoms. Found 14 (27 requested) and removed 19 (14 requested) atoms. Cycle 9: After refmac, R = 0.2115 (Rfree = 0.000) for 3162 atoms. Found 11 (26 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.2108 (Rfree = 0.000) for 3141 atoms. Found 15 (26 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.68 2.87 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 64 residues added (7 deleted due to clashes), 3285 seeds are put forward Round 1: 263 peptides, 36 chains. Longest chain 17 peptides. Score 0.598 Round 2: 277 peptides, 32 chains. Longest chain 19 peptides. Score 0.678 Round 3: 290 peptides, 32 chains. Longest chain 18 peptides. Score 0.706 Round 4: 298 peptides, 33 chains. Longest chain 27 peptides. Score 0.713 Round 5: 288 peptides, 30 chains. Longest chain 19 peptides. Score 0.721 Taking the results from Round 5 Chains 30, Residues 258, Estimated correctness of the model 69.5 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7184 restraints for refining 3213 atoms. 6157 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2321 (Rfree = 0.000) for 3213 atoms. Found 21 (25 requested) and removed 21 (14 requested) atoms. Cycle 12: After refmac, R = 0.2182 (Rfree = 0.000) for 3211 atoms. Found 12 (25 requested) and removed 19 (14 requested) atoms. Cycle 13: After refmac, R = 0.2211 (Rfree = 0.000) for 3200 atoms. Found 6 (24 requested) and removed 19 (14 requested) atoms. Cycle 14: After refmac, R = 0.2087 (Rfree = 0.000) for 3185 atoms. Found 10 (24 requested) and removed 14 (14 requested) atoms. Cycle 15: After refmac, R = 0.2078 (Rfree = 0.000) for 3179 atoms. Found 5 (23 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.65 2.83 Search for helices and strands: 0 residues in 0 chains, 3253 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3272 seeds are put forward Round 1: 239 peptides, 35 chains. Longest chain 17 peptides. Score 0.541 Round 2: 272 peptides, 34 chains. Longest chain 16 peptides. Score 0.644 Round 3: 274 peptides, 35 chains. Longest chain 23 peptides. Score 0.638 Round 4: 271 peptides, 34 chains. Longest chain 17 peptides. Score 0.642 Round 5: 292 peptides, 30 chains. Longest chain 24 peptides. Score 0.729 Taking the results from Round 5 Chains 33, Residues 262, Estimated correctness of the model 71.1 % 4 chains (63 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 121 A and 132 A 31 chains (271 residues) following loop building 3 chains (73 residues) in sequence following loop building ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6124 restraints for refining 3213 atoms. 4764 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2387 (Rfree = 0.000) for 3213 atoms. Found 22 (22 requested) and removed 23 (14 requested) atoms. Cycle 17: After refmac, R = 0.2123 (Rfree = 0.000) for 3201 atoms. Found 8 (22 requested) and removed 16 (14 requested) atoms. Cycle 18: After refmac, R = 0.2112 (Rfree = 0.000) for 3188 atoms. Found 8 (21 requested) and removed 16 (14 requested) atoms. Cycle 19: After refmac, R = 0.2107 (Rfree = 0.000) for 3174 atoms. Found 9 (21 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.2024 (Rfree = 0.000) for 3166 atoms. Found 11 (20 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.66 2.84 Search for helices and strands: 0 residues in 0 chains, 3245 seeds are put forward NCS extension: 44 residues added (7 deleted due to clashes), 3289 seeds are put forward Round 1: 231 peptides, 38 chains. Longest chain 16 peptides. Score 0.474 Round 2: 257 peptides, 31 chains. Longest chain 17 peptides. Score 0.641 Round 3: 261 peptides, 33 chains. Longest chain 27 peptides. Score 0.628 Round 4: 254 peptides, 30 chains. Longest chain 18 peptides. Score 0.645 Round 5: 272 peptides, 33 chains. Longest chain 21 peptides. Score 0.655 Taking the results from Round 5 Chains 33, Residues 239, Estimated correctness of the model 55.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7253 restraints for refining 3213 atoms. 6330 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2221 (Rfree = 0.000) for 3213 atoms. Found 17 (20 requested) and removed 14 (14 requested) atoms. Cycle 22: After refmac, R = 0.2022 (Rfree = 0.000) for 3211 atoms. Found 3 (20 requested) and removed 14 (14 requested) atoms. Cycle 23: After refmac, R = 0.1974 (Rfree = 0.000) for 3198 atoms. Found 2 (20 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.1933 (Rfree = 0.000) for 3184 atoms. Found 4 (20 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.1904 (Rfree = 0.000) for 3174 atoms. Found 3 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.64 2.82 Search for helices and strands: 0 residues in 0 chains, 3244 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3270 seeds are put forward Round 1: 232 peptides, 36 chains. Longest chain 13 peptides. Score 0.506 Round 2: 258 peptides, 30 chains. Longest chain 16 peptides. Score 0.654 Round 3: 259 peptides, 28 chains. Longest chain 19 peptides. Score 0.679 Round 4: 257 peptides, 33 chains. Longest chain 15 peptides. Score 0.617 Round 5: 250 peptides, 32 chains. Longest chain 18 peptides. Score 0.611 Taking the results from Round 3 Chains 29, Residues 231, Estimated correctness of the model 60.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7214 restraints for refining 3213 atoms. 6288 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2135 (Rfree = 0.000) for 3213 atoms. Found 15 (20 requested) and removed 16 (14 requested) atoms. Cycle 27: After refmac, R = 0.1998 (Rfree = 0.000) for 3211 atoms. Found 6 (20 requested) and removed 14 (14 requested) atoms. Cycle 28: After refmac, R = 0.1919 (Rfree = 0.000) for 3203 atoms. Found 5 (20 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.1901 (Rfree = 0.000) for 3193 atoms. Found 5 (20 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.1889 (Rfree = 0.000) for 3183 atoms. Found 4 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.64 2.82 Search for helices and strands: 0 residues in 0 chains, 3238 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3260 seeds are put forward Round 1: 247 peptides, 39 chains. Longest chain 15 peptides. Score 0.512 Round 2: 262 peptides, 34 chains. Longest chain 20 peptides. Score 0.619 Round 3: 260 peptides, 37 chains. Longest chain 21 peptides. Score 0.577 Round 4: 251 peptides, 36 chains. Longest chain 18 peptides. Score 0.564 Round 5: 263 peptides, 36 chains. Longest chain 25 peptides. Score 0.598 Taking the results from Round 2 Chains 36, Residues 228, Estimated correctness of the model 46.1 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6841 restraints for refining 3213 atoms. 5829 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2123 (Rfree = 0.000) for 3213 atoms. Found 20 (20 requested) and removed 18 (14 requested) atoms. Cycle 32: After refmac, R = 0.1985 (Rfree = 0.000) for 3209 atoms. Found 14 (20 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.1912 (Rfree = 0.000) for 3209 atoms. Found 6 (20 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.1909 (Rfree = 0.000) for 3200 atoms. Found 7 (20 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.1891 (Rfree = 0.000) for 3191 atoms. Found 4 (20 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.66 2.84 Search for helices and strands: 0 residues in 0 chains, 3244 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3271 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 9 peptides. Score 0.374 Round 2: 231 peptides, 34 chains. Longest chain 18 peptides. Score 0.530 Round 3: 227 peptides, 37 chains. Longest chain 14 peptides. Score 0.475 Round 4: 239 peptides, 34 chains. Longest chain 16 peptides. Score 0.554 Round 5: 243 peptides, 39 chains. Longest chain 15 peptides. Score 0.499 Taking the results from Round 4 Chains 34, Residues 205, Estimated correctness of the model 28.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7447 restraints for refining 3213 atoms. 6661 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2014 (Rfree = 0.000) for 3213 atoms. Found 15 (20 requested) and removed 14 (14 requested) atoms. Cycle 37: After refmac, R = 0.1863 (Rfree = 0.000) for 3212 atoms. Found 5 (20 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.1844 (Rfree = 0.000) for 3200 atoms. Found 8 (20 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.1804 (Rfree = 0.000) for 3191 atoms. Found 7 (20 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.1779 (Rfree = 0.000) for 3181 atoms. Found 4 (20 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.65 2.83 Search for helices and strands: 0 residues in 0 chains, 3249 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3262 seeds are put forward Round 1: 199 peptides, 36 chains. Longest chain 14 peptides. Score 0.392 Round 2: 220 peptides, 33 chains. Longest chain 19 peptides. Score 0.509 Round 3: 223 peptides, 29 chains. Longest chain 16 peptides. Score 0.573 Round 4: 208 peptides, 29 chains. Longest chain 22 peptides. Score 0.527 Round 5: 219 peptides, 33 chains. Longest chain 15 peptides. Score 0.506 Taking the results from Round 3 Chains 31, Residues 194, Estimated correctness of the model 33.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7343 restraints for refining 3213 atoms. 6559 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1931 (Rfree = 0.000) for 3213 atoms. Found 11 (20 requested) and removed 16 (14 requested) atoms. Cycle 42: After refmac, R = 0.1788 (Rfree = 0.000) for 3205 atoms. Found 1 (20 requested) and removed 14 (14 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 3188 atoms. Found 6 (20 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.1789 (Rfree = 0.000) for 3180 atoms. Found 5 (20 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.1799 (Rfree = 0.000) for 3169 atoms. Found 7 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3232 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3253 seeds are put forward Round 1: 181 peptides, 31 chains. Longest chain 16 peptides. Score 0.404 Round 2: 215 peptides, 30 chains. Longest chain 22 peptides. Score 0.535 Round 3: 220 peptides, 35 chains. Longest chain 13 peptides. Score 0.481 Round 4: 228 peptides, 32 chains. Longest chain 16 peptides. Score 0.548 Round 5: 224 peptides, 29 chains. Longest chain 17 peptides. Score 0.576 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 195, Estimated correctness of the model 34.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vjn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6759 reflections ( 98.21 % complete ) and 7374 restraints for refining 3202 atoms. 6623 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1923 (Rfree = 0.000) for 3202 atoms. Found 0 (20 requested) and removed 13 (14 requested) atoms. Cycle 47: After refmac, R = 0.1856 (Rfree = 0.000) for 3186 atoms. Found 0 (20 requested) and removed 9 (14 requested) atoms. Cycle 48: After refmac, R = 0.1884 (Rfree = 0.000) for 3177 atoms. Found 0 (20 requested) and removed 2 (14 requested) atoms. Cycle 49: After refmac, R = 0.1849 (Rfree = 0.000) for 3174 atoms. TimeTaking 42.37