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 2o08-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o08-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o08-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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/2o08-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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/2o08-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-4.0-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 333 and 0 Target number of residues in the AU: 333 Target solvent content: 0.6691 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-4.0-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.95 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: 83.235 4.000 Wilson plot Bfac: 91.80 4727 reflections ( 97.24 % complete ) and 0 restraints for refining 3348 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3474 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3546 (Rfree = 0.000) for 3348 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.02 3.37 Search for helices and strands: 0 residues in 0 chains, 3425 seeds are put forward NCS extension: 0 residues added, 3425 seeds are put forward Round 1: 139 peptides, 28 chains. Longest chain 8 peptides. Score 0.270 Round 2: 169 peptides, 24 chains. Longest chain 15 peptides. Score 0.426 Round 3: 174 peptides, 22 chains. Longest chain 16 peptides. Score 0.467 Round 4: 185 peptides, 23 chains. Longest chain 16 peptides. Score 0.485 Round 5: 187 peptides, 20 chains. Longest chain 20 peptides. Score 0.528 Taking the results from Round 5 Chains 20, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6275 restraints for refining 2699 atoms. 5627 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2582 (Rfree = 0.000) for 2699 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 2: After refmac, R = 0.2386 (Rfree = 0.000) for 2649 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 3: After refmac, R = 0.2334 (Rfree = 0.000) for 2629 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.2346 (Rfree = 0.000) for 2616 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2311 (Rfree = 0.000) for 2605 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.20 Search for helices and strands: 0 residues in 0 chains, 2735 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2750 seeds are put forward Round 1: 181 peptides, 27 chains. Longest chain 15 peptides. Score 0.421 Round 2: 180 peptides, 23 chains. Longest chain 16 peptides. Score 0.471 Round 3: 203 peptides, 24 chains. Longest chain 17 peptides. Score 0.520 Round 4: 206 peptides, 22 chains. Longest chain 20 peptides. Score 0.552 Round 5: 205 peptides, 20 chains. Longest chain 17 peptides. Score 0.573 Taking the results from Round 5 Chains 20, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6074 restraints for refining 2696 atoms. 5354 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3162 (Rfree = 0.000) for 2696 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 7: After refmac, R = 0.2488 (Rfree = 0.000) for 2686 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2393 (Rfree = 0.000) for 2686 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2409 (Rfree = 0.000) for 2671 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.2303 (Rfree = 0.000) for 2664 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.22 Search for helices and strands: 0 residues in 0 chains, 2779 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2799 seeds are put forward Round 1: 163 peptides, 29 chains. Longest chain 11 peptides. Score 0.337 Round 2: 188 peptides, 26 chains. Longest chain 14 peptides. Score 0.454 Round 3: 200 peptides, 27 chains. Longest chain 19 peptides. Score 0.475 Round 4: 202 peptides, 27 chains. Longest chain 14 peptides. Score 0.481 Round 5: 207 peptides, 27 chains. Longest chain 18 peptides. Score 0.494 Taking the results from Round 5 Chains 27, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6111 restraints for refining 2717 atoms. 5418 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2409 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 12: After refmac, R = 0.2061 (Rfree = 0.000) for 2682 atoms. Found 7 (12 requested) and removed 19 (6 requested) atoms. Cycle 13: After refmac, R = 0.1952 (Rfree = 0.000) for 2653 atoms. Found 5 (12 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.1915 (Rfree = 0.000) for 2632 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1939 (Rfree = 0.000) for 2623 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.13 Search for helices and strands: 0 residues in 0 chains, 2720 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2739 seeds are put forward Round 1: 168 peptides, 31 chains. Longest chain 10 peptides. Score 0.325 Round 2: 183 peptides, 26 chains. Longest chain 15 peptides. Score 0.440 Round 3: 200 peptides, 29 chains. Longest chain 16 peptides. Score 0.450 Round 4: 196 peptides, 29 chains. Longest chain 14 peptides. Score 0.438 Round 5: 201 peptides, 30 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 3 Chains 30, Residues 171, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6082 restraints for refining 2717 atoms. 5393 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2563 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 35 (6 requested) atoms. Cycle 17: After refmac, R = 0.2387 (Rfree = 0.000) for 2657 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.2178 (Rfree = 0.000) for 2618 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.2107 (Rfree = 0.000) for 2600 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1782 (Rfree = 0.000) for 2587 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 3.20 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward NCS extension: 0 residues added, 2710 seeds are put forward Round 1: 163 peptides, 32 chains. Longest chain 8 peptides. Score 0.294 Round 2: 183 peptides, 29 chains. Longest chain 14 peptides. Score 0.400 Round 3: 198 peptides, 32 chains. Longest chain 14 peptides. Score 0.405 Round 4: 200 peptides, 30 chains. Longest chain 13 peptides. Score 0.437 Round 5: 194 peptides, 28 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 5 Chains 28, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6133 restraints for refining 2717 atoms. 5497 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2453 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 22: After refmac, R = 0.2232 (Rfree = 0.000) for 2688 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 23: After refmac, R = 0.2152 (Rfree = 0.000) for 2675 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2090 (Rfree = 0.000) for 2663 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 25: After refmac, R = 0.1700 (Rfree = 0.000) for 2655 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 3.20 Search for helices and strands: 0 residues in 0 chains, 2775 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 2791 seeds are put forward Round 1: 154 peptides, 28 chains. Longest chain 10 peptides. Score 0.322 Round 2: 185 peptides, 30 chains. Longest chain 12 peptides. Score 0.393 Round 3: 181 peptides, 27 chains. Longest chain 14 peptides. Score 0.421 Round 4: 171 peptides, 26 chains. Longest chain 13 peptides. Score 0.404 Round 5: 170 peptides, 27 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 3 Chains 27, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6172 restraints for refining 2717 atoms. 5583 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2202 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2282 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2211 (Rfree = 0.000) for 2685 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2084 (Rfree = 0.000) for 2660 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.2193 (Rfree = 0.000) for 2649 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.20 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2794 seeds are put forward Round 1: 134 peptides, 28 chains. Longest chain 9 peptides. Score 0.252 Round 2: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.342 Round 3: 183 peptides, 32 chains. Longest chain 11 peptides. Score 0.359 Round 4: 172 peptides, 29 chains. Longest chain 14 peptides. Score 0.366 Round 5: 170 peptides, 28 chains. Longest chain 11 peptides. Score 0.373 Taking the results from Round 5 Chains 28, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6201 restraints for refining 2716 atoms. 5661 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2506 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2327 (Rfree = 0.000) for 2688 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.2212 (Rfree = 0.000) for 2675 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 34: After refmac, R = 0.2003 (Rfree = 0.000) for 2656 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 35: After refmac, R = 0.2110 (Rfree = 0.000) for 2649 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.20 Search for helices and strands: 0 residues in 0 chains, 2739 seeds are put forward NCS extension: 0 residues added, 2739 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 8 peptides. Score 0.225 Round 2: 148 peptides, 28 chains. Longest chain 14 peptides. Score 0.301 Round 3: 142 peptides, 25 chains. Longest chain 13 peptides. Score 0.325 Round 4: 159 peptides, 28 chains. Longest chain 12 peptides. Score 0.338 Round 5: 141 peptides, 22 chains. Longest chain 13 peptides. Score 0.367 Taking the results from Round 5 Chains 22, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6467 restraints for refining 2716 atoms. 6013 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2407 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 37: After refmac, R = 0.2107 (Rfree = 0.000) for 2684 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.2238 (Rfree = 0.000) for 2677 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.2092 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.1746 (Rfree = 0.000) for 2663 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.19 Search for helices and strands: 0 residues in 0 chains, 2771 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2791 seeds are put forward Round 1: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.269 Round 2: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.343 Round 3: 165 peptides, 28 chains. Longest chain 11 peptides. Score 0.358 Round 4: 158 peptides, 28 chains. Longest chain 9 peptides. Score 0.335 Round 5: 173 peptides, 28 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 5 Chains 28, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4727 reflections ( 97.24 % complete ) and 6296 restraints for refining 2716 atoms. 5744 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2367 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 42: After refmac, R = 0.2296 (Rfree = 0.000) for 2686 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.2047 (Rfree = 0.000) for 2680 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 44: After refmac, R = 0.2126 (Rfree = 0.000) for 2675 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 45: After refmac, R = 0.1911 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 2755 seeds are put forward NCS extension: 0 residues added, 2755 seeds are put forward Round 1: 136 peptides, 30 chains. Longest chain 9 peptides. Score 0.228 Round 2: 160 peptides, 30 chains. Longest chain 11 peptides. Score 0.313 Round 3: 164 peptides, 24 chains. Longest chain 15 peptides. Score 0.410 Round 4: 164 peptides, 27 chains. Longest chain 13 peptides. Score 0.368 Round 5: 155 peptides, 26 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 140, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2o08-4_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (140 residues) following loop building 3 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4727 reflections ( 97.24 % complete ) and 5957 restraints for refining 2717 atoms. 5315 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2245 (Rfree = 0.000) for 2717 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2360 (Rfree = 0.000) for 2690 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2268 (Rfree = 0.000) for 2674 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2192 (Rfree = 0.000) for 2661 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:20:47 GMT 2018 Job finished. TimeTaking 52.83 Used memory is bytes: 19534808