null Sun 23 Dec 22:22:59 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 1vmi-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.8-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/1vmi-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.8-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 ============================================================ Sun 23 Dec 22:23:07 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/1vmi-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-3.8-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 281 and 0 Target number of residues in the AU: 281 Target solvent content: 0.6629 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.57 Input MTZ file: 1vmi-3.8-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: 182 Cell parameters: 94.674 94.674 174.359 90.000 90.000 120.000 Input sequence file: 1vmi-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 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 Loops will be built when appropriate and at the last cycle Resolution range: 87.180 3.800 Wilson plot Bfac: 86.35 4967 reflections ( 99.58 % complete ) and 0 restraints for refining 3147 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3408 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3898 (Rfree = 0.000) for 3147 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.45 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward Round 1: 122 peptides, 23 chains. Longest chain 13 peptides. Score 0.302 Round 2: 162 peptides, 24 chains. Longest chain 16 peptides. Score 0.437 Round 3: 177 peptides, 21 chains. Longest chain 18 peptides. Score 0.532 Round 4: 187 peptides, 20 chains. Longest chain 23 peptides. Score 0.575 Round 5: 185 peptides, 17 chains. Longest chain 23 peptides. Score 0.609 Taking the results from Round 5 Chains 21, Residues 168, Estimated correctness of the model 3.0 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 5278 restraints for refining 2484 atoms. 4468 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3211 (Rfree = 0.000) for 2484 atoms. Found 13 (13 requested) and removed 45 (6 requested) atoms. Cycle 2: After refmac, R = 0.3067 (Rfree = 0.000) for 2357 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 3: After refmac, R = 0.3075 (Rfree = 0.000) for 2300 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.3055 (Rfree = 0.000) for 2270 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 5: After refmac, R = 0.2973 (Rfree = 0.000) for 2243 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.40 Search for helices and strands: 0 residues in 0 chains, 2328 seeds are put forward Round 1: 175 peptides, 26 chains. Longest chain 18 peptides. Score 0.451 Round 2: 190 peptides, 22 chains. Longest chain 20 peptides. Score 0.557 Round 3: 193 peptides, 19 chains. Longest chain 24 peptides. Score 0.605 Round 4: 201 peptides, 18 chains. Longest chain 26 peptides. Score 0.638 Round 5: 190 peptides, 18 chains. Longest chain 26 peptides. Score 0.610 Taking the results from Round 4 Chains 21, Residues 183, Estimated correctness of the model 15.8 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 4901 restraints for refining 2349 atoms. 4091 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3125 (Rfree = 0.000) for 2349 atoms. Found 12 (12 requested) and removed 39 (6 requested) atoms. Cycle 7: After refmac, R = 0.3074 (Rfree = 0.000) for 2276 atoms. Found 12 (12 requested) and removed 40 (6 requested) atoms. Cycle 8: After refmac, R = 0.3017 (Rfree = 0.000) for 2218 atoms. Found 12 (12 requested) and removed 35 (6 requested) atoms. Cycle 9: After refmac, R = 0.2676 (Rfree = 0.000) for 2158 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 10: After refmac, R = 0.2753 (Rfree = 0.000) for 2123 atoms. Found 11 (11 requested) and removed 39 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 2201 seeds are put forward Round 1: 190 peptides, 29 chains. Longest chain 15 peptides. Score 0.457 Round 2: 193 peptides, 22 chains. Longest chain 24 peptides. Score 0.565 Round 3: 192 peptides, 23 chains. Longest chain 20 peptides. Score 0.549 Round 4: 195 peptides, 25 chains. Longest chain 23 peptides. Score 0.530 Round 5: 192 peptides, 22 chains. Longest chain 20 peptides. Score 0.563 Taking the results from Round 2 Chains 23, Residues 171, Estimated correctness of the model 0.0 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 4360 restraints for refining 2266 atoms. 3492 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3133 (Rfree = 0.000) for 2266 atoms. Found 12 (12 requested) and removed 48 (6 requested) atoms. Cycle 12: After refmac, R = 0.3023 (Rfree = 0.000) for 2187 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 13: After refmac, R = 0.2934 (Rfree = 0.000) for 2146 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 14: After refmac, R = 0.2906 (Rfree = 0.000) for 2124 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. Cycle 15: After refmac, R = 0.2866 (Rfree = 0.000) for 2096 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward Round 1: 177 peptides, 25 chains. Longest chain 17 peptides. Score 0.473 Round 2: 182 peptides, 24 chains. Longest chain 20 peptides. Score 0.504 Round 3: 183 peptides, 22 chains. Longest chain 27 peptides. Score 0.536 Round 4: 188 peptides, 19 chains. Longest chain 35 peptides. Score 0.591 Round 5: 188 peptides, 22 chains. Longest chain 24 peptides. Score 0.551 Taking the results from Round 4 Chains 22, Residues 169, Estimated correctness of the model 0.0 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 4441 restraints for refining 2337 atoms. 3574 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3240 (Rfree = 0.000) for 2337 atoms. Found 12 (12 requested) and removed 60 (6 requested) atoms. Cycle 17: After refmac, R = 0.3075 (Rfree = 0.000) for 2249 atoms. Found 12 (12 requested) and removed 37 (6 requested) atoms. Cycle 18: After refmac, R = 0.2944 (Rfree = 0.000) for 2199 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 19: After refmac, R = 0.2631 (Rfree = 0.000) for 2164 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. Cycle 20: After refmac, R = 0.2923 (Rfree = 0.000) for 2142 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward Round 1: 167 peptides, 29 chains. Longest chain 12 peptides. Score 0.376 Round 2: 192 peptides, 27 chains. Longest chain 17 peptides. Score 0.493 Round 3: 182 peptides, 22 chains. Longest chain 25 peptides. Score 0.533 Round 4: 183 peptides, 23 chains. Longest chain 16 peptides. Score 0.522 Round 5: 201 peptides, 24 chains. Longest chain 19 peptides. Score 0.562 Taking the results from Round 5 Chains 30, Residues 177, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 4579 restraints for refining 2388 atoms. 3724 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3083 (Rfree = 0.000) for 2388 atoms. Found 12 (13 requested) and removed 18 (6 requested) atoms. Cycle 22: After refmac, R = 0.3007 (Rfree = 0.000) for 2329 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 23: After refmac, R = 0.2851 (Rfree = 0.000) for 2283 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 24: After refmac, R = 0.2798 (Rfree = 0.000) for 2244 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2814 (Rfree = 0.000) for 2217 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 2314 seeds are put forward Round 1: 193 peptides, 30 chains. Longest chain 13 peptides. Score 0.453 Round 2: 200 peptides, 22 chains. Longest chain 32 peptides. Score 0.585 Round 3: 190 peptides, 25 chains. Longest chain 17 peptides. Score 0.515 Round 4: 189 peptides, 25 chains. Longest chain 17 peptides. Score 0.512 Round 5: 201 peptides, 25 chains. Longest chain 20 peptides. Score 0.548 Taking the results from Round 2 Chains 27, Residues 178, Estimated correctness of the model 0.0 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 4560 restraints for refining 2356 atoms. 3734 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3102 (Rfree = 0.000) for 2356 atoms. Found 12 (12 requested) and removed 35 (6 requested) atoms. Cycle 27: After refmac, R = 0.2958 (Rfree = 0.000) for 2296 atoms. Found 10 (12 requested) and removed 31 (6 requested) atoms. Cycle 28: After refmac, R = 0.2739 (Rfree = 0.000) for 2254 atoms. Found 10 (12 requested) and removed 20 (6 requested) atoms. Cycle 29: After refmac, R = 0.2667 (Rfree = 0.000) for 2230 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 30: After refmac, R = 0.2298 (Rfree = 0.000) for 2213 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward Round 1: 164 peptides, 28 chains. Longest chain 13 peptides. Score 0.381 Round 2: 182 peptides, 22 chains. Longest chain 26 peptides. Score 0.533 Round 3: 170 peptides, 23 chains. Longest chain 19 peptides. Score 0.480 Round 4: 181 peptides, 21 chains. Longest chain 40 peptides. Score 0.544 Round 5: 176 peptides, 22 chains. Longest chain 26 peptides. Score 0.514 Taking the results from Round 4 Chains 25, Residues 160, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 4926 restraints for refining 2386 atoms. 4160 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2999 (Rfree = 0.000) for 2386 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 32: After refmac, R = 0.2770 (Rfree = 0.000) for 2327 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 33: After refmac, R = 0.2757 (Rfree = 0.000) for 2291 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 34: After refmac, R = 0.2731 (Rfree = 0.000) for 2268 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 35: After refmac, R = 0.2648 (Rfree = 0.000) for 2239 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 2343 seeds are put forward Round 1: 166 peptides, 28 chains. Longest chain 14 peptides. Score 0.389 Round 2: 182 peptides, 25 chains. Longest chain 14 peptides. Score 0.490 Round 3: 193 peptides, 24 chains. Longest chain 18 peptides. Score 0.538 Round 4: 192 peptides, 23 chains. Longest chain 19 peptides. Score 0.549 Round 5: 192 peptides, 24 chains. Longest chain 28 peptides. Score 0.535 Taking the results from Round 4 Chains 26, Residues 169, Estimated correctness of the model 0.0 % 6 chains (46 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 4828 restraints for refining 2418 atoms. 4034 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2984 (Rfree = 0.000) for 2418 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 37: After refmac, R = 0.2803 (Rfree = 0.000) for 2368 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2875 (Rfree = 0.000) for 2330 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2713 (Rfree = 0.000) for 2297 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 40: After refmac, R = 0.2310 (Rfree = 0.000) for 2278 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 2383 seeds are put forward Round 1: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.389 Round 2: 169 peptides, 24 chains. Longest chain 21 peptides. Score 0.462 Round 3: 175 peptides, 21 chains. Longest chain 31 peptides. Score 0.525 Round 4: 165 peptides, 22 chains. Longest chain 18 peptides. Score 0.478 Round 5: 160 peptides, 19 chains. Longest chain 18 peptides. Score 0.507 Taking the results from Round 3 Chains 24, Residues 154, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 4967 reflections ( 99.58 % complete ) and 5031 restraints for refining 2461 atoms. 4312 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3022 (Rfree = 0.000) for 2461 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 42: After refmac, R = 0.2917 (Rfree = 0.000) for 2409 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. Cycle 43: After refmac, R = 0.2735 (Rfree = 0.000) for 2360 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 44: After refmac, R = 0.2730 (Rfree = 0.000) for 2318 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 45: After refmac, R = 0.2767 (Rfree = 0.000) for 2299 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 2407 seeds are put forward Round 1: 128 peptides, 22 chains. Longest chain 13 peptides. Score 0.344 Round 2: 168 peptides, 27 chains. Longest chain 16 peptides. Score 0.412 Round 3: 156 peptides, 24 chains. Longest chain 14 peptides. Score 0.416 Round 4: 169 peptides, 26 chains. Longest chain 15 peptides. Score 0.431 Round 5: 170 peptides, 25 chains. Longest chain 18 peptides. Score 0.450 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 145, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vmi-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4967 reflections ( 99.58 % complete ) and 5146 restraints for refining 2374 atoms. 4537 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2981 (Rfree = 0.000) for 2374 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2758 (Rfree = 0.000) for 2337 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2921 (Rfree = 0.000) for 2309 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2929 (Rfree = 0.000) for 2292 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:17 GMT 2018 Job finished. TimeTaking 55.31 Used memory is bytes: 18872776