null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjn-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.2-parrot-hancs/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-hancs.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-hancs.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 3872 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.2839 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2101 (Rfree = 0.000) for 3872 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.68 2.87 Search for helices and strands: 0 residues in 0 chains, 3927 seeds are put forward NCS extension: 0 residues added, 3927 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 10 peptides. Score 0.374 Round 2: 249 peptides, 38 chains. Longest chain 15 peptides. Score 0.532 Round 3: 238 peptides, 33 chains. Longest chain 20 peptides. Score 0.565 Round 4: 255 peptides, 35 chains. Longest chain 17 peptides. Score 0.588 Round 5: 265 peptides, 33 chains. Longest chain 18 peptides. Score 0.638 Taking the results from Round 5 Chains 34, Residues 232, Estimated correctness of the model 50.9 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6880 restraints for refining 3211 atoms. 5924 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2337 (Rfree = 0.000) for 3211 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 2: After refmac, R = 0.2166 (Rfree = 0.000) for 3192 atoms. Found 18 (28 requested) and removed 18 (14 requested) atoms. Cycle 3: After refmac, R = 0.2086 (Rfree = 0.000) for 3175 atoms. Found 12 (28 requested) and removed 16 (14 requested) atoms. Cycle 4: After refmac, R = 0.2062 (Rfree = 0.000) for 3168 atoms. Found 13 (28 requested) and removed 15 (14 requested) atoms. Cycle 5: After refmac, R = 0.1997 (Rfree = 0.000) for 3163 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.68 2.87 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 3239 seeds are put forward Round 1: 230 peptides, 36 chains. Longest chain 19 peptides. Score 0.499 Round 2: 254 peptides, 33 chains. Longest chain 17 peptides. Score 0.609 Round 3: 263 peptides, 33 chains. Longest chain 18 peptides. Score 0.633 Round 4: 283 peptides, 33 chains. Longest chain 28 peptides. Score 0.681 Round 5: 284 peptides, 31 chains. Longest chain 28 peptides. Score 0.703 Taking the results from Round 5 Chains 35, Residues 253, Estimated correctness of the model 65.8 % 3 chains (51 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 68 A 34 chains (257 residues) following loop building 2 chains (55 residues) in sequence following loop building ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6402 restraints for refining 3213 atoms. 5184 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2373 (Rfree = 0.000) for 3213 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 7: After refmac, R = 0.2225 (Rfree = 0.000) for 3204 atoms. Found 18 (27 requested) and removed 17 (14 requested) atoms. Cycle 8: After refmac, R = 0.2233 (Rfree = 0.000) for 3196 atoms. Found 16 (27 requested) and removed 15 (14 requested) atoms. Cycle 9: After refmac, R = 0.2544 (Rfree = 0.000) for 3194 atoms. Found 26 (26 requested) and removed 25 (14 requested) atoms. Cycle 10: After refmac, R = 0.2162 (Rfree = 0.000) for 3170 atoms. Found 18 (26 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.65 2.83 Search for helices and strands: 0 residues in 0 chains, 3239 seeds are put forward NCS extension: 50 residues added (4 deleted due to clashes), 3289 seeds are put forward Round 1: 244 peptides, 32 chains. Longest chain 28 peptides. Score 0.594 Round 2: 273 peptides, 33 chains. Longest chain 28 peptides. Score 0.658 Round 3: 273 peptides, 27 chains. Longest chain 28 peptides. Score 0.719 Round 4: 278 peptides, 30 chains. Longest chain 28 peptides. Score 0.700 Round 5: 278 peptides, 30 chains. Longest chain 28 peptides. Score 0.700 Taking the results from Round 3 Chains 28, Residues 246, Estimated correctness of the model 69.1 % 2 chains (38 residues) have been docked in sequence Building loops using Loopy2018 28 chains (246 residues) following loop building 2 chains (38 residues) in sequence following loop building ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6598 restraints for refining 3153 atoms. 5485 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2407 (Rfree = 0.000) for 3153 atoms. Found 25 (25 requested) and removed 23 (14 requested) atoms. Cycle 12: After refmac, R = 0.2226 (Rfree = 0.000) for 3149 atoms. Found 25 (25 requested) and removed 22 (14 requested) atoms. Cycle 13: After refmac, R = 0.2102 (Rfree = 0.000) for 3147 atoms. Found 12 (24 requested) and removed 15 (14 requested) atoms. Cycle 14: After refmac, R = 0.2048 (Rfree = 0.000) for 3141 atoms. Found 10 (24 requested) and removed 14 (14 requested) atoms. Cycle 15: After refmac, R = 0.2055 (Rfree = 0.000) for 3130 atoms. Found 9 (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, 3177 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 3206 seeds are put forward Round 1: 242 peptides, 30 chains. Longest chain 28 peptides. Score 0.613 Round 2: 266 peptides, 28 chains. Longest chain 29 peptides. Score 0.694 Round 3: 276 peptides, 30 chains. Longest chain 29 peptides. Score 0.696 Round 4: 277 peptides, 26 chains. Longest chain 32 peptides. Score 0.737 Round 5: 275 peptides, 30 chains. Longest chain 28 peptides. Score 0.694 Taking the results from Round 4 Chains 29, Residues 251, Estimated correctness of the model 72.6 % 3 chains (58 residues) have been docked in sequence Building loops using Loopy2018 29 chains (251 residues) following loop building 3 chains (58 residues) in sequence following loop building ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6426 restraints for refining 3207 atoms. 5188 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2398 (Rfree = 0.000) for 3207 atoms. Found 22 (22 requested) and removed 24 (14 requested) atoms. Cycle 17: After refmac, R = 0.2220 (Rfree = 0.000) for 3199 atoms. Found 15 (22 requested) and removed 20 (14 requested) atoms. Cycle 18: After refmac, R = 0.2133 (Rfree = 0.000) for 3189 atoms. Found 5 (21 requested) and removed 14 (14 requested) atoms. Cycle 19: After refmac, R = 0.2102 (Rfree = 0.000) for 3179 atoms. Found 7 (21 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.2070 (Rfree = 0.000) for 3169 atoms. Found 4 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 31 residues added (9 deleted due to clashes), 3248 seeds are put forward Round 1: 243 peptides, 32 chains. Longest chain 24 peptides. Score 0.592 Round 2: 276 peptides, 26 chains. Longest chain 34 peptides. Score 0.735 Round 3: 268 peptides, 29 chains. Longest chain 25 peptides. Score 0.689 Round 4: 260 peptides, 26 chains. Longest chain 35 peptides. Score 0.702 Round 5: 250 peptides, 28 chains. Longest chain 20 peptides. Score 0.657 Taking the results from Round 2 Chains 27, Residues 250, Estimated correctness of the model 72.3 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6728 restraints for refining 3213 atoms. 5610 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2304 (Rfree = 0.000) for 3213 atoms. Found 15 (20 requested) and removed 23 (14 requested) atoms. Cycle 22: After refmac, R = 0.2165 (Rfree = 0.000) for 3199 atoms. Found 9 (19 requested) and removed 16 (14 requested) atoms. Cycle 23: After refmac, R = 0.2105 (Rfree = 0.000) for 3189 atoms. Found 2 (18 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.2077 (Rfree = 0.000) for 3174 atoms. Found 5 (18 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.2045 (Rfree = 0.000) for 3164 atoms. Found 4 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 22 residues added (15 deleted due to clashes), 3212 seeds are put forward Round 1: 254 peptides, 33 chains. Longest chain 24 peptides. Score 0.609 Round 2: 260 peptides, 31 chains. Longest chain 28 peptides. Score 0.648 Round 3: 254 peptides, 36 chains. Longest chain 19 peptides. Score 0.572 Round 4: 249 peptides, 29 chains. Longest chain 25 peptides. Score 0.643 Round 5: 268 peptides, 32 chains. Longest chain 23 peptides. Score 0.657 Taking the results from Round 5 Chains 32, Residues 236, Estimated correctness of the model 55.5 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 6925 restraints for refining 3213 atoms. 5906 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2280 (Rfree = 0.000) for 3213 atoms. Found 17 (17 requested) and removed 16 (14 requested) atoms. Cycle 27: After refmac, R = 0.2137 (Rfree = 0.000) for 3208 atoms. Found 14 (17 requested) and removed 17 (14 requested) atoms. Cycle 28: After refmac, R = 0.2059 (Rfree = 0.000) for 3202 atoms. Found 7 (17 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.2011 (Rfree = 0.000) for 3192 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.1975 (Rfree = 0.000) for 3183 atoms. Found 2 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.63 2.81 Search for helices and strands: 0 residues in 0 chains, 3244 seeds are put forward NCS extension: 27 residues added (6 deleted due to clashes), 3271 seeds are put forward Round 1: 212 peptides, 32 chains. Longest chain 19 peptides. Score 0.497 Round 2: 248 peptides, 32 chains. Longest chain 23 peptides. Score 0.605 Round 3: 251 peptides, 33 chains. Longest chain 23 peptides. Score 0.601 Round 4: 264 peptides, 34 chains. Longest chain 21 peptides. Score 0.624 Round 5: 238 peptides, 30 chains. Longest chain 19 peptides. Score 0.603 Taking the results from Round 4 Chains 34, Residues 230, Estimated correctness of the model 47.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7270 restraints for refining 3212 atoms. 6384 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2220 (Rfree = 0.000) for 3212 atoms. Found 17 (17 requested) and removed 16 (14 requested) atoms. Cycle 32: After refmac, R = 0.2069 (Rfree = 0.000) for 3208 atoms. Found 10 (17 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2008 (Rfree = 0.000) for 3203 atoms. Found 8 (17 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.1972 (Rfree = 0.000) for 3196 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.1934 (Rfree = 0.000) for 3182 atoms. Found 13 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.65 2.83 Search for helices and strands: 0 residues in 0 chains, 3256 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3282 seeds are put forward Round 1: 215 peptides, 33 chains. Longest chain 12 peptides. Score 0.493 Round 2: 242 peptides, 31 chains. Longest chain 23 peptides. Score 0.601 Round 3: 231 peptides, 31 chains. Longest chain 23 peptides. Score 0.570 Round 4: 236 peptides, 27 chains. Longest chain 23 peptides. Score 0.634 Round 5: 230 peptides, 28 chains. Longest chain 23 peptides. Score 0.605 Taking the results from Round 4 Chains 27, Residues 209, Estimated correctness of the model 49.9 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7034 restraints for refining 3212 atoms. 6098 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2086 (Rfree = 0.000) for 3212 atoms. Found 17 (17 requested) and removed 20 (14 requested) atoms. Cycle 37: After refmac, R = 0.1963 (Rfree = 0.000) for 3204 atoms. Found 12 (17 requested) and removed 17 (14 requested) atoms. Cycle 38: After refmac, R = 0.1903 (Rfree = 0.000) for 3196 atoms. Found 7 (17 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.1873 (Rfree = 0.000) for 3184 atoms. Found 7 (17 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.1832 (Rfree = 0.000) for 3173 atoms. Found 5 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.64 2.82 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 3251 seeds are put forward Round 1: 199 peptides, 33 chains. Longest chain 11 peptides. Score 0.438 Round 2: 218 peptides, 29 chains. Longest chain 21 peptides. Score 0.558 Round 3: 219 peptides, 28 chains. Longest chain 22 peptides. Score 0.574 Round 4: 216 peptides, 27 chains. Longest chain 17 peptides. Score 0.579 Round 5: 224 peptides, 28 chains. Longest chain 17 peptides. Score 0.589 Taking the results from Round 5 Chains 28, Residues 196, Estimated correctness of the model 38.1 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6759 reflections ( 98.21 % complete ) and 7422 restraints for refining 3200 atoms. 6623 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2131 (Rfree = 0.000) for 3200 atoms. Found 16 (17 requested) and removed 15 (14 requested) atoms. Cycle 42: After refmac, R = 0.2004 (Rfree = 0.000) for 3198 atoms. Found 4 (17 requested) and removed 14 (14 requested) atoms. Cycle 43: After refmac, R = 0.1956 (Rfree = 0.000) for 3185 atoms. Found 6 (17 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.1940 (Rfree = 0.000) for 3175 atoms. Found 3 (17 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.1902 (Rfree = 0.000) for 3163 atoms. Found 8 (17 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.59 2.77 Search for helices and strands: 0 residues in 0 chains, 3230 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3249 seeds are put forward Round 1: 190 peptides, 33 chains. Longest chain 15 peptides. Score 0.406 Round 2: 222 peptides, 30 chains. Longest chain 16 peptides. Score 0.556 Round 3: 231 peptides, 33 chains. Longest chain 17 peptides. Score 0.544 Round 4: 226 peptides, 30 chains. Longest chain 17 peptides. Score 0.568 Round 5: 221 peptides, 33 chains. Longest chain 27 peptides. Score 0.512 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 196, Estimated correctness of the model 32.1 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 6 % 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 7314 restraints for refining 3213 atoms. 6503 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2061 (Rfree = 0.000) for 3213 atoms. Found 0 (17 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1973 (Rfree = 0.000) for 3198 atoms. Found 0 (17 requested) and removed 7 (14 requested) atoms. Cycle 48: After refmac, R = 0.1982 (Rfree = 0.000) for 3188 atoms. Found 0 (17 requested) and removed 5 (14 requested) atoms. Cycle 49: After refmac, R = 0.1920 (Rfree = 0.000) for 3183 atoms. Found 0 (17 requested) and removed 4 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:27:49 GMT 2018 Job finished. TimeTaking 59.88 Used memory is bytes: 18963560