Mon 24 Dec 00:24:24 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 2pbl-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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/2pbl-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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 00:24:28 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/2pbl-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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 656 and 0 Target number of residues in the AU: 656 Target solvent content: 0.6484 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-3.8-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 77.07 9891 reflections ( 98.93 % complete ) and 0 restraints for refining 9250 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3611 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4146 (Rfree = 0.000) for 9250 atoms. Found 50 (50 requested) and removed 78 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.72 Search for helices and strands: 0 residues in 0 chains, 9459 seeds are put forward NCS extension: 0 residues added, 9459 seeds are put forward Round 1: 264 peptides, 59 chains. Longest chain 9 peptides. Score 0.224 Round 2: 369 peptides, 74 chains. Longest chain 11 peptides. Score 0.302 Round 3: 408 peptides, 74 chains. Longest chain 11 peptides. Score 0.368 Round 4: 431 peptides, 76 chains. Longest chain 15 peptides. Score 0.392 Round 5: 458 peptides, 77 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 5 Chains 79, Residues 381, Estimated correctness of the model 0.0 % 12 chains (80 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 17397 restraints for refining 7584 atoms. 15709 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3797 (Rfree = 0.000) for 7584 atoms. Found 41 (41 requested) and removed 77 (20 requested) atoms. Cycle 2: After refmac, R = 0.3664 (Rfree = 0.000) for 7357 atoms. Found 41 (41 requested) and removed 44 (20 requested) atoms. Cycle 3: After refmac, R = 0.3039 (Rfree = 0.000) for 7250 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. Cycle 4: After refmac, R = 0.3507 (Rfree = 0.000) for 7193 atoms. Found 39 (39 requested) and removed 33 (19 requested) atoms. Cycle 5: After refmac, R = 0.3526 (Rfree = 0.000) for 7143 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7431 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 7455 seeds are put forward Round 1: 387 peptides, 76 chains. Longest chain 11 peptides. Score 0.319 Round 2: 455 peptides, 77 chains. Longest chain 15 peptides. Score 0.423 Round 3: 472 peptides, 72 chains. Longest chain 15 peptides. Score 0.480 Round 4: 487 peptides, 74 chains. Longest chain 27 peptides. Score 0.489 Round 5: 520 peptides, 81 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 5 Chains 83, Residues 439, Estimated correctness of the model 0.0 % 14 chains (90 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16146 restraints for refining 7314 atoms. 14207 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3343 (Rfree = 0.000) for 7314 atoms. Found 40 (40 requested) and removed 108 (20 requested) atoms. Cycle 7: After refmac, R = 0.3283 (Rfree = 0.000) for 7116 atoms. Found 39 (39 requested) and removed 66 (19 requested) atoms. Cycle 8: After refmac, R = 0.3213 (Rfree = 0.000) for 7013 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Cycle 9: After refmac, R = 0.3112 (Rfree = 0.000) for 6942 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 10: After refmac, R = 0.2367 (Rfree = 0.000) for 6904 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 7193 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 7205 seeds are put forward Round 1: 400 peptides, 78 chains. Longest chain 23 peptides. Score 0.327 Round 2: 490 peptides, 84 chains. Longest chain 15 peptides. Score 0.430 Round 3: 497 peptides, 81 chains. Longest chain 15 peptides. Score 0.460 Round 4: 521 peptides, 80 chains. Longest chain 25 peptides. Score 0.500 Round 5: 517 peptides, 80 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 4 Chains 80, Residues 441, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16026 restraints for refining 7150 atoms. 14293 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3104 (Rfree = 0.000) for 7150 atoms. Found 39 (39 requested) and removed 77 (19 requested) atoms. Cycle 12: After refmac, R = 0.3049 (Rfree = 0.000) for 7042 atoms. Found 39 (39 requested) and removed 71 (19 requested) atoms. Cycle 13: After refmac, R = 0.2866 (Rfree = 0.000) for 6949 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. Cycle 14: After refmac, R = 0.2254 (Rfree = 0.000) for 6897 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 15: After refmac, R = 0.2584 (Rfree = 0.000) for 6886 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 7200 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 7224 seeds are put forward Round 1: 407 peptides, 82 chains. Longest chain 10 peptides. Score 0.310 Round 2: 481 peptides, 85 chains. Longest chain 18 peptides. Score 0.410 Round 3: 488 peptides, 77 chains. Longest chain 19 peptides. Score 0.472 Round 4: 478 peptides, 79 chains. Longest chain 14 peptides. Score 0.444 Round 5: 502 peptides, 74 chains. Longest chain 19 peptides. Score 0.510 Taking the results from Round 5 Chains 77, Residues 428, Estimated correctness of the model 0.0 % 8 chains (58 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 15891 restraints for refining 7240 atoms. 14067 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3140 (Rfree = 0.000) for 7240 atoms. Found 39 (39 requested) and removed 103 (19 requested) atoms. Cycle 17: After refmac, R = 0.2854 (Rfree = 0.000) for 7089 atoms. Found 39 (39 requested) and removed 50 (19 requested) atoms. Cycle 18: After refmac, R = 0.2642 (Rfree = 0.000) for 7029 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 19: After refmac, R = 0.2608 (Rfree = 0.000) for 6997 atoms. Found 38 (38 requested) and removed 38 (19 requested) atoms. Cycle 20: After refmac, R = 0.2560 (Rfree = 0.000) for 6966 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7266 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 7301 seeds are put forward Round 1: 383 peptides, 79 chains. Longest chain 9 peptides. Score 0.290 Round 2: 453 peptides, 79 chains. Longest chain 13 peptides. Score 0.406 Round 3: 474 peptides, 79 chains. Longest chain 13 peptides. Score 0.439 Round 4: 479 peptides, 73 chains. Longest chain 14 peptides. Score 0.484 Round 5: 477 peptides, 74 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 4 Chains 74, Residues 406, Estimated correctness of the model 0.0 % 11 chains (62 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 15967 restraints for refining 7267 atoms. 14249 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2916 (Rfree = 0.000) for 7267 atoms. Found 39 (39 requested) and removed 80 (19 requested) atoms. Cycle 22: After refmac, R = 0.2634 (Rfree = 0.000) for 7168 atoms. Found 39 (39 requested) and removed 46 (19 requested) atoms. Cycle 23: After refmac, R = 0.2641 (Rfree = 0.000) for 7111 atoms. Found 39 (39 requested) and removed 43 (19 requested) atoms. Cycle 24: After refmac, R = 0.2533 (Rfree = 0.000) for 7069 atoms. Found 39 (39 requested) and removed 27 (19 requested) atoms. Cycle 25: After refmac, R = 0.1863 (Rfree = 0.000) for 7055 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 7354 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7372 seeds are put forward Round 1: 381 peptides, 82 chains. Longest chain 9 peptides. Score 0.265 Round 2: 450 peptides, 81 chains. Longest chain 12 peptides. Score 0.388 Round 3: 451 peptides, 79 chains. Longest chain 13 peptides. Score 0.403 Round 4: 475 peptides, 78 chains. Longest chain 15 peptides. Score 0.446 Round 5: 490 peptides, 78 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 5 Chains 78, Residues 412, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16099 restraints for refining 7225 atoms. 14444 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2795 (Rfree = 0.000) for 7225 atoms. Found 39 (39 requested) and removed 84 (19 requested) atoms. Cycle 27: After refmac, R = 0.2630 (Rfree = 0.000) for 7123 atoms. Found 39 (39 requested) and removed 43 (19 requested) atoms. Cycle 28: After refmac, R = 0.2527 (Rfree = 0.000) for 7073 atoms. Found 39 (39 requested) and removed 34 (19 requested) atoms. Cycle 29: After refmac, R = 0.1811 (Rfree = 0.000) for 7042 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 30: After refmac, R = 0.1596 (Rfree = 0.000) for 7045 atoms. Found 14 (38 requested) and removed 29 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 7285 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 7296 seeds are put forward Round 1: 335 peptides, 73 chains. Longest chain 10 peptides. Score 0.249 Round 2: 412 peptides, 74 chains. Longest chain 10 peptides. Score 0.375 Round 3: 422 peptides, 70 chains. Longest chain 19 peptides. Score 0.418 Round 4: 411 peptides, 71 chains. Longest chain 19 peptides. Score 0.394 Round 5: 431 peptides, 68 chains. Longest chain 24 peptides. Score 0.446 Taking the results from Round 5 Chains 69, Residues 363, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16889 restraints for refining 7378 atoms. 15448 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2621 (Rfree = 0.000) for 7378 atoms. Found 40 (40 requested) and removed 74 (20 requested) atoms. Cycle 32: After refmac, R = 0.2655 (Rfree = 0.000) for 7293 atoms. Found 40 (40 requested) and removed 48 (20 requested) atoms. Cycle 33: After refmac, R = 0.2571 (Rfree = 0.000) for 7244 atoms. Found 40 (40 requested) and removed 50 (20 requested) atoms. Cycle 34: After refmac, R = 0.2472 (Rfree = 0.000) for 7199 atoms. Found 39 (39 requested) and removed 31 (19 requested) atoms. Cycle 35: After refmac, R = 0.2556 (Rfree = 0.000) for 7180 atoms. Found 39 (39 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.79 Search for helices and strands: 0 residues in 0 chains, 7477 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7492 seeds are put forward Round 1: 266 peptides, 57 chains. Longest chain 7 peptides. Score 0.244 Round 2: 372 peptides, 71 chains. Longest chain 13 peptides. Score 0.330 Round 3: 396 peptides, 65 chains. Longest chain 27 peptides. Score 0.412 Round 4: 404 peptides, 70 chains. Longest chain 19 peptides. Score 0.390 Round 5: 419 peptides, 69 chains. Longest chain 24 peptides. Score 0.421 Taking the results from Round 5 Chains 71, Residues 350, Estimated correctness of the model 0.0 % 7 chains (69 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16144 restraints for refining 7323 atoms. 14604 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2927 (Rfree = 0.000) for 7323 atoms. Found 40 (40 requested) and removed 74 (20 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2759 (Rfree = 0.000) for 7218 atoms. Found 40 (40 requested) and removed 46 (20 requested) atoms. Cycle 38: After refmac, R = 0.2634 (Rfree = 0.000) for 7164 atoms. Found 39 (39 requested) and removed 45 (19 requested) atoms. Cycle 39: After refmac, R = 0.2501 (Rfree = 0.000) for 7123 atoms. Found 39 (39 requested) and removed 33 (19 requested) atoms. Cycle 40: After refmac, R = 0.1783 (Rfree = 0.000) for 7110 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 7329 seeds are put forward NCS extension: 27 residues added (7 deleted due to clashes), 7356 seeds are put forward Round 1: 321 peptides, 72 chains. Longest chain 7 peptides. Score 0.231 Round 2: 389 peptides, 73 chains. Longest chain 12 peptides. Score 0.344 Round 3: 367 peptides, 69 chains. Longest chain 12 peptides. Score 0.336 Round 4: 359 peptides, 62 chains. Longest chain 16 peptides. Score 0.373 Round 5: 377 peptides, 68 chains. Longest chain 16 peptides. Score 0.360 Taking the results from Round 4 Chains 62, Residues 297, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9891 reflections ( 98.93 % complete ) and 16665 restraints for refining 7220 atoms. 15449 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2840 (Rfree = 0.000) for 7220 atoms. Found 39 (39 requested) and removed 58 (19 requested) atoms. Cycle 42: After refmac, R = 0.2850 (Rfree = 0.000) for 7158 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 43: After refmac, R = 0.2962 (Rfree = 0.000) for 7119 atoms. Found 39 (39 requested) and removed 32 (19 requested) atoms. Cycle 44: After refmac, R = 0.2944 (Rfree = 0.000) for 7084 atoms. Found 39 (39 requested) and removed 30 (19 requested) atoms. Cycle 45: After refmac, R = 0.3003 (Rfree = 0.000) for 7066 atoms. Found 39 (39 requested) and removed 29 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.79 Search for helices and strands: 0 residues in 0 chains, 7257 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 7281 seeds are put forward Round 1: 264 peptides, 62 chains. Longest chain 7 peptides. Score 0.200 Round 2: 333 peptides, 68 chains. Longest chain 9 peptides. Score 0.283 Round 3: 339 peptides, 65 chains. Longest chain 11 peptides. Score 0.317 Round 4: 322 peptides, 60 chains. Longest chain 12 peptides. Score 0.324 Round 5: 328 peptides, 63 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 262, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (262 residues) following loop building 5 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9891 reflections ( 98.93 % complete ) and 15665 restraints for refining 6911 atoms. 14615 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3111 (Rfree = 0.000) for 6911 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.3227 (Rfree = 0.000) for 6846 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.3047 (Rfree = 0.000) for 6789 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.3064 (Rfree = 0.000) for 6740 atoms. TimeTaking 67.3