Sun 23 Dec 22:23:07 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 2pbl-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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/2pbl-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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 ============================================================ Sun 23 Dec 22:23:17 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/2pbl-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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 635 and 0 Target number of residues in the AU: 635 Target solvent content: 0.6597 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.75 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: 87.858 4.000 Wilson plot Bfac: 84.56 8486 reflections ( 98.79 % complete ) and 0 restraints for refining 9291 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3688 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4202 (Rfree = 0.000) for 9291 atoms. Found 44 (44 requested) and removed 119 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.90 Search for helices and strands: 0 residues in 0 chains, 9400 seeds are put forward NCS extension: 0 residues added, 9400 seeds are put forward Round 1: 235 peptides, 54 chains. Longest chain 7 peptides. Score 0.207 Round 2: 326 peptides, 68 chains. Longest chain 10 peptides. Score 0.271 Round 3: 352 peptides, 71 chains. Longest chain 8 peptides. Score 0.295 Round 4: 372 peptides, 71 chains. Longest chain 12 peptides. Score 0.330 Round 5: 372 peptides, 69 chains. Longest chain 10 peptides. Score 0.344 Taking the results from Round 5 Chains 69, Residues 303, Estimated correctness of the model 0.0 % 7 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 18398 restraints for refining 7568 atoms. 17176 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3713 (Rfree = 0.000) for 7568 atoms. Found 35 (35 requested) and removed 86 (17 requested) atoms. Cycle 2: After refmac, R = 0.3585 (Rfree = 0.000) for 7346 atoms. Found 35 (35 requested) and removed 58 (17 requested) atoms. Cycle 3: After refmac, R = 0.3527 (Rfree = 0.000) for 7235 atoms. Found 34 (34 requested) and removed 58 (17 requested) atoms. Cycle 4: After refmac, R = 0.3445 (Rfree = 0.000) for 7135 atoms. Found 34 (34 requested) and removed 38 (17 requested) atoms. Cycle 5: After refmac, R = 0.2737 (Rfree = 0.000) for 7072 atoms. Found 33 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 7287 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 7297 seeds are put forward Round 1: 325 peptides, 69 chains. Longest chain 9 peptides. Score 0.261 Round 2: 388 peptides, 64 chains. Longest chain 14 peptides. Score 0.406 Round 3: 439 peptides, 75 chains. Longest chain 15 peptides. Score 0.411 Round 4: 430 peptides, 71 chains. Longest chain 14 peptides. Score 0.424 Round 5: 440 peptides, 73 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 5 Chains 74, Residues 367, Estimated correctness of the model 0.0 % 10 chains (57 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 16228 restraints for refining 7092 atoms. 14678 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3193 (Rfree = 0.000) for 7092 atoms. Found 33 (33 requested) and removed 100 (16 requested) atoms. Cycle 7: After refmac, R = 0.3169 (Rfree = 0.000) for 6915 atoms. Found 33 (33 requested) and removed 47 (16 requested) atoms. Cycle 8: After refmac, R = 0.3065 (Rfree = 0.000) for 6829 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 9: After refmac, R = 0.3065 (Rfree = 0.000) for 6773 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 10: After refmac, R = 0.3049 (Rfree = 0.000) for 6726 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 6975 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6990 seeds are put forward Round 1: 326 peptides, 71 chains. Longest chain 10 peptides. Score 0.248 Round 2: 415 peptides, 74 chains. Longest chain 11 peptides. Score 0.380 Round 3: 431 peptides, 69 chains. Longest chain 15 peptides. Score 0.439 Round 4: 424 peptides, 70 chains. Longest chain 14 peptides. Score 0.422 Round 5: 429 peptides, 68 chains. Longest chain 18 peptides. Score 0.443 Taking the results from Round 5 Chains 68, Residues 361, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15771 restraints for refining 6942 atoms. 14349 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3101 (Rfree = 0.000) for 6942 atoms. Found 33 (33 requested) and removed 76 (16 requested) atoms. Cycle 12: After refmac, R = 0.3069 (Rfree = 0.000) for 6821 atoms. Found 32 (32 requested) and removed 50 (16 requested) atoms. Cycle 13: After refmac, R = 0.2984 (Rfree = 0.000) for 6737 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2980 (Rfree = 0.000) for 6691 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 15: After refmac, R = 0.2923 (Rfree = 0.000) for 6652 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 6853 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6867 seeds are put forward Round 1: 327 peptides, 73 chains. Longest chain 8 peptides. Score 0.234 Round 2: 393 peptides, 67 chains. Longest chain 18 peptides. Score 0.393 Round 3: 396 peptides, 67 chains. Longest chain 12 peptides. Score 0.398 Round 4: 405 peptides, 68 chains. Longest chain 14 peptides. Score 0.405 Round 5: 413 peptides, 69 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 5 Chains 69, Residues 344, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15640 restraints for refining 6840 atoms. 14291 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3118 (Rfree = 0.000) for 6840 atoms. Found 32 (32 requested) and removed 79 (16 requested) atoms. Cycle 17: After refmac, R = 0.2961 (Rfree = 0.000) for 6731 atoms. Found 32 (32 requested) and removed 53 (16 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2899 (Rfree = 0.000) for 6667 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2073 (Rfree = 0.000) for 6630 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 20: After refmac, R = 0.1952 (Rfree = 0.000) for 6622 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 6885 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6902 seeds are put forward Round 1: 327 peptides, 71 chains. Longest chain 12 peptides. Score 0.249 Round 2: 396 peptides, 76 chains. Longest chain 13 peptides. Score 0.334 Round 3: 413 peptides, 75 chains. Longest chain 12 peptides. Score 0.370 Round 4: 412 peptides, 72 chains. Longest chain 14 peptides. Score 0.389 Round 5: 396 peptides, 70 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 4 Chains 73, Residues 340, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15284 restraints for refining 6821 atoms. 13880 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2967 (Rfree = 0.000) for 6821 atoms. Found 32 (32 requested) and removed 67 (16 requested) atoms. Cycle 22: After refmac, R = 0.2945 (Rfree = 0.000) for 6730 atoms. Found 32 (32 requested) and removed 48 (16 requested) atoms. Cycle 23: After refmac, R = 0.2771 (Rfree = 0.000) for 6681 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 24: After refmac, R = 0.2149 (Rfree = 0.000) for 6646 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 25: After refmac, R = 0.1937 (Rfree = 0.000) for 6622 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 6808 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6826 seeds are put forward Round 1: 328 peptides, 66 chains. Longest chain 9 peptides. Score 0.290 Round 2: 373 peptides, 70 chains. Longest chain 13 peptides. Score 0.339 Round 3: 375 peptides, 67 chains. Longest chain 18 peptides. Score 0.364 Round 4: 366 peptides, 67 chains. Longest chain 12 peptides. Score 0.349 Round 5: 346 peptides, 66 chains. Longest chain 14 peptides. Score 0.321 Taking the results from Round 3 Chains 67, Residues 308, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8486 reflections ( 98.79 % complete ) and 15381 restraints for refining 6727 atoms. 14159 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2970 (Rfree = 0.000) for 6727 atoms. Found 31 (31 requested) and removed 59 (15 requested) atoms. Cycle 27: After refmac, R = 0.3054 (Rfree = 0.000) for 6643 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 28: After refmac, R = 0.2922 (Rfree = 0.000) for 6607 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 29: After refmac, R = 0.2192 (Rfree = 0.000) for 6571 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 30: After refmac, R = 0.1934 (Rfree = 0.000) for 6569 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 6753 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 6787 seeds are put forward Round 1: 288 peptides, 63 chains. Longest chain 7 peptides. Score 0.239 Round 2: 372 peptides, 73 chains. Longest chain 10 peptides. Score 0.315 Round 3: 363 peptides, 69 chains. Longest chain 11 peptides. Score 0.329 Round 4: 361 peptides, 68 chains. Longest chain 13 peptides. Score 0.333 Round 5: 372 peptides, 68 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 5 Chains 68, Residues 304, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15568 restraints for refining 6692 atoms. 14420 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2890 (Rfree = 0.000) for 6692 atoms. Found 31 (31 requested) and removed 71 (15 requested) atoms. Cycle 32: After refmac, R = 0.2805 (Rfree = 0.000) for 6606 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 33: After refmac, R = 0.2831 (Rfree = 0.000) for 6552 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 34: After refmac, R = 0.2783 (Rfree = 0.000) for 6522 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 35: After refmac, R = 0.2003 (Rfree = 0.000) for 6510 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 6720 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6734 seeds are put forward Round 1: 283 peptides, 61 chains. Longest chain 9 peptides. Score 0.245 Round 2: 335 peptides, 67 chains. Longest chain 9 peptides. Score 0.294 Round 3: 341 peptides, 62 chains. Longest chain 11 peptides. Score 0.342 Round 4: 341 peptides, 62 chains. Longest chain 14 peptides. Score 0.342 Round 5: 329 peptides, 57 chains. Longest chain 12 peptides. Score 0.359 Taking the results from Round 5 Chains 57, Residues 272, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15156 restraints for refining 6704 atoms. 14025 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2928 (Rfree = 0.000) for 6704 atoms. Found 31 (31 requested) and removed 66 (15 requested) atoms. Cycle 37: After refmac, R = 0.2883 (Rfree = 0.000) for 6602 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 38: After refmac, R = 0.2096 (Rfree = 0.000) for 6547 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 39: After refmac, R = 0.1836 (Rfree = 0.000) for 6521 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 40: After refmac, R = 0.1709 (Rfree = 0.000) for 6519 atoms. Found 31 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 6723 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6738 seeds are put forward Round 1: 278 peptides, 60 chains. Longest chain 8 peptides. Score 0.243 Round 2: 314 peptides, 62 chains. Longest chain 10 peptides. Score 0.295 Round 3: 319 peptides, 57 chains. Longest chain 12 peptides. Score 0.342 Round 4: 322 peptides, 55 chains. Longest chain 13 peptides. Score 0.362 Round 5: 317 peptides, 58 chains. Longest chain 12 peptides. Score 0.331 Taking the results from Round 4 Chains 55, Residues 267, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15120 restraints for refining 6599 atoms. 14082 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2763 (Rfree = 0.000) for 6599 atoms. Found 31 (31 requested) and removed 62 (15 requested) atoms. Cycle 42: After refmac, R = 0.2921 (Rfree = 0.000) for 6526 atoms. Found 31 (31 requested) and removed 50 (15 requested) atoms. Cycle 43: After refmac, R = 0.2871 (Rfree = 0.000) for 6491 atoms. Found 30 (30 requested) and removed 48 (15 requested) atoms. Cycle 44: After refmac, R = 0.2957 (Rfree = 0.000) for 6454 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 45: After refmac, R = 0.2806 (Rfree = 0.000) for 6433 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.91 Search for helices and strands: 0 residues in 0 chains, 6629 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 6644 seeds are put forward Round 1: 255 peptides, 53 chains. Longest chain 12 peptides. Score 0.256 Round 2: 269 peptides, 48 chains. Longest chain 11 peptides. Score 0.323 Round 3: 287 peptides, 51 chains. Longest chain 12 peptides. Score 0.332 Round 4: 277 peptides, 48 chains. Longest chain 11 peptides. Score 0.337 Round 5: 262 peptides, 45 chains. Longest chain 15 peptides. Score 0.334 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 229, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2pbl-4_warpNtrace.pdb as input Building loops using Loopy2018 48 chains (229 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8486 reflections ( 98.79 % complete ) and 14353 restraints for refining 6361 atoms. 13456 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2990 (Rfree = 0.000) for 6361 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.3001 (Rfree = 0.000) for 6314 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2772 (Rfree = 0.000) for 6278 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2917 (Rfree = 0.000) for 6240 atoms. TimeTaking 86