Sun 23 Dec 22:22:46 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 2o5r-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-2.3-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/2o5r-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-2.3-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 22:22:56 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/2o5r-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-2.3-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 757 and 0 Target number of residues in the AU: 757 Target solvent content: 0.4893 Checking the provided sequence file Detected sequence length: 481 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 962 Adjusted target solvent content: 0.35 Input MTZ file: 2o5r-2.3-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: 152 Cell parameters: 69.953 69.953 283.945 90.000 90.000 120.000 Input sequence file: 2o5r-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 7696 target number of atoms Had to go as low as 0.45 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: 19.992 2.340 Wilson plot Bfac: 21.28 34670 reflections ( 98.47 % complete ) and 0 restraints for refining 8475 atoms. Observations/parameters ratio is 1.02 ------------------------------------------------------ Starting model: R = 0.3467 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3747 (Rfree = 0.000) for 8475 atoms. Found 94 (185 requested) and removed 273 (92 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 4.58 NCS extension: 0 residues added, 8296 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 6 peptides. Score 0.230 Round 2: 207 peptides, 40 chains. Longest chain 8 peptides. Score 0.288 Round 3: 239 peptides, 42 chains. Longest chain 10 peptides. Score 0.342 Round 4: 272 peptides, 46 chains. Longest chain 13 peptides. Score 0.375 Round 5: 252 peptides, 40 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 5 Chains 40, Residues 212, Estimated correctness of the model 52.5 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 15214 restraints for refining 6317 atoms. 14376 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3874 (Rfree = 0.000) for 6317 atoms. Found 93 (138 requested) and removed 202 (69 requested) atoms. Cycle 2: After refmac, R = 0.3744 (Rfree = 0.000) for 6101 atoms. Found 60 (135 requested) and removed 123 (67 requested) atoms. Cycle 3: After refmac, R = 0.3484 (Rfree = 0.000) for 5959 atoms. Found 72 (132 requested) and removed 113 (66 requested) atoms. Cycle 4: After refmac, R = 0.3395 (Rfree = 0.000) for 5873 atoms. Found 55 (129 requested) and removed 88 (64 requested) atoms. Cycle 5: After refmac, R = 0.3275 (Rfree = 0.000) for 5804 atoms. Found 51 (127 requested) and removed 73 (63 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.37 2.91 NCS extension: 0 residues added, 5801 seeds are put forward Round 1: 243 peptides, 50 chains. Longest chain 9 peptides. Score 0.273 Round 2: 262 peptides, 46 chains. Longest chain 16 peptides. Score 0.354 Round 3: 301 peptides, 49 chains. Longest chain 16 peptides. Score 0.408 Round 4: 293 peptides, 44 chains. Longest chain 16 peptides. Score 0.436 Round 5: 296 peptides, 49 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 4 Chains 44, Residues 249, Estimated correctness of the model 59.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 11699 restraints for refining 5409 atoms. 10747 conditional restraints added. Observations/parameters ratio is 1.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3353 (Rfree = 0.000) for 5409 atoms. Found 70 (118 requested) and removed 76 (59 requested) atoms. Cycle 7: After refmac, R = 0.3394 (Rfree = 0.000) for 5387 atoms. Found 80 (118 requested) and removed 90 (59 requested) atoms. Cycle 8: After refmac, R = 0.3055 (Rfree = 0.000) for 5339 atoms. Found 48 (117 requested) and removed 66 (58 requested) atoms. Cycle 9: After refmac, R = 0.2982 (Rfree = 0.000) for 5301 atoms. Found 45 (116 requested) and removed 64 (58 requested) atoms. Cycle 10: After refmac, R = 0.2925 (Rfree = 0.000) for 5271 atoms. Found 25 (115 requested) and removed 61 (57 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.26 2.78 NCS extension: 0 residues added, 5294 seeds are put forward Round 1: 265 peptides, 49 chains. Longest chain 15 peptides. Score 0.332 Round 2: 299 peptides, 49 chains. Longest chain 14 peptides. Score 0.404 Round 3: 297 peptides, 46 chains. Longest chain 14 peptides. Score 0.426 Round 4: 290 peptides, 47 chains. Longest chain 11 peptides. Score 0.403 Round 5: 303 peptides, 45 chains. Longest chain 21 peptides. Score 0.447 Taking the results from Round 5 Chains 45, Residues 258, Estimated correctness of the model 60.4 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 11078 restraints for refining 5300 atoms. 10066 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3506 (Rfree = 0.000) for 5300 atoms. Found 106 (116 requested) and removed 96 (58 requested) atoms. Cycle 12: After refmac, R = 0.3046 (Rfree = 0.000) for 5279 atoms. Found 74 (116 requested) and removed 64 (58 requested) atoms. Cycle 13: After refmac, R = 0.2949 (Rfree = 0.000) for 5249 atoms. Found 59 (115 requested) and removed 62 (57 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2924 (Rfree = 0.000) for 5226 atoms. Found 52 (114 requested) and removed 65 (57 requested) atoms. Cycle 15: After refmac, R = 0.2888 (Rfree = 0.000) for 5199 atoms. Found 49 (114 requested) and removed 61 (57 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.21 2.72 NCS extension: 0 residues added, 5208 seeds are put forward Round 1: 275 peptides, 51 chains. Longest chain 11 peptides. Score 0.335 Round 2: 300 peptides, 48 chains. Longest chain 17 peptides. Score 0.414 Round 3: 301 peptides, 49 chains. Longest chain 14 peptides. Score 0.408 Round 4: 311 peptides, 51 chains. Longest chain 16 peptides. Score 0.410 Round 5: 318 peptides, 47 chains. Longest chain 16 peptides. Score 0.458 Taking the results from Round 5 Chains 47, Residues 271, Estimated correctness of the model 61.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 10950 restraints for refining 5319 atoms. 9851 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3351 (Rfree = 0.000) for 5319 atoms. Found 94 (116 requested) and removed 75 (58 requested) atoms. Cycle 17: After refmac, R = 0.3210 (Rfree = 0.000) for 5318 atoms. Found 86 (116 requested) and removed 70 (58 requested) atoms. Cycle 18: After refmac, R = 0.3219 (Rfree = 0.000) for 5316 atoms. Found 109 (116 requested) and removed 73 (58 requested) atoms. Cycle 19: After refmac, R = 0.3159 (Rfree = 0.000) for 5336 atoms. Found 75 (117 requested) and removed 68 (58 requested) atoms. Cycle 20: After refmac, R = 0.3132 (Rfree = 0.000) for 5319 atoms. Found 87 (117 requested) and removed 68 (58 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.22 2.73 NCS extension: 3 residues added (0 deleted due to clashes), 5355 seeds are put forward Round 1: 284 peptides, 48 chains. Longest chain 18 peptides. Score 0.382 Round 2: 299 peptides, 40 chains. Longest chain 22 peptides. Score 0.482 Round 3: 298 peptides, 45 chains. Longest chain 19 peptides. Score 0.437 Round 4: 315 peptides, 44 chains. Longest chain 30 peptides. Score 0.478 Round 5: 310 peptides, 45 chains. Longest chain 21 peptides. Score 0.460 Taking the results from Round 2 Chains 41, Residues 259, Estimated correctness of the model 64.9 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 10902 restraints for refining 5393 atoms. 9809 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3017 (Rfree = 0.000) for 5393 atoms. Found 101 (118 requested) and removed 72 (59 requested) atoms. Cycle 22: After refmac, R = 0.3054 (Rfree = 0.000) for 5413 atoms. Found 82 (118 requested) and removed 67 (59 requested) atoms. Cycle 23: After refmac, R = 0.3045 (Rfree = 0.000) for 5402 atoms. Found 78 (118 requested) and removed 60 (59 requested) atoms. Cycle 24: After refmac, R = 0.2802 (Rfree = 0.000) for 5385 atoms. Found 36 (118 requested) and removed 62 (59 requested) atoms. Cycle 25: After refmac, R = 0.2754 (Rfree = 0.000) for 5341 atoms. Found 28 (117 requested) and removed 62 (58 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.18 2.68 NCS extension: 0 residues added, 5334 seeds are put forward Round 1: 262 peptides, 46 chains. Longest chain 20 peptides. Score 0.354 Round 2: 301 peptides, 45 chains. Longest chain 23 peptides. Score 0.443 Round 3: 283 peptides, 44 chains. Longest chain 19 peptides. Score 0.416 Round 4: 293 peptides, 44 chains. Longest chain 21 peptides. Score 0.436 Round 5: 282 peptides, 43 chains. Longest chain 22 peptides. Score 0.423 Taking the results from Round 2 Chains 47, Residues 256, Estimated correctness of the model 59.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 10778 restraints for refining 5275 atoms. 9735 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3076 (Rfree = 0.000) for 5275 atoms. Found 100 (115 requested) and removed 67 (57 requested) atoms. Cycle 27: After refmac, R = 0.3027 (Rfree = 0.000) for 5291 atoms. Found 98 (116 requested) and removed 63 (58 requested) atoms. Cycle 28: After refmac, R = 0.2990 (Rfree = 0.000) for 5312 atoms. Found 88 (116 requested) and removed 65 (58 requested) atoms. Cycle 29: After refmac, R = 0.2734 (Rfree = 0.000) for 5324 atoms. Found 37 (116 requested) and removed 62 (58 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2689 (Rfree = 0.000) for 5288 atoms. Found 38 (116 requested) and removed 60 (58 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.17 2.67 NCS extension: 0 residues added, 5275 seeds are put forward Round 1: 273 peptides, 50 chains. Longest chain 14 peptides. Score 0.340 Round 2: 288 peptides, 45 chains. Longest chain 21 peptides. Score 0.417 Round 3: 288 peptides, 44 chains. Longest chain 19 peptides. Score 0.426 Round 4: 275 peptides, 39 chains. Longest chain 27 peptides. Score 0.445 Round 5: 281 peptides, 41 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 4 Chains 39, Residues 236, Estimated correctness of the model 60.2 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 11014 restraints for refining 5371 atoms. 9979 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2998 (Rfree = 0.000) for 5371 atoms. Found 103 (117 requested) and removed 68 (58 requested) atoms. Cycle 32: After refmac, R = 0.2991 (Rfree = 0.000) for 5399 atoms. Found 105 (118 requested) and removed 66 (59 requested) atoms. Cycle 33: After refmac, R = 0.2685 (Rfree = 0.000) for 5427 atoms. Found 50 (119 requested) and removed 61 (59 requested) atoms. Cycle 34: After refmac, R = 0.2633 (Rfree = 0.000) for 5402 atoms. Found 38 (118 requested) and removed 62 (59 requested) atoms. Cycle 35: After refmac, R = 0.2577 (Rfree = 0.000) for 5373 atoms. Found 34 (117 requested) and removed 58 (58 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.17 2.67 NCS extension: 7 residues added (0 deleted due to clashes), 5367 seeds are put forward Round 1: 266 peptides, 48 chains. Longest chain 11 peptides. Score 0.344 Round 2: 295 peptides, 44 chains. Longest chain 19 peptides. Score 0.440 Round 3: 277 peptides, 40 chains. Longest chain 18 peptides. Score 0.440 Round 4: 291 peptides, 45 chains. Longest chain 14 peptides. Score 0.423 Round 5: 289 peptides, 45 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 3 Chains 42, Residues 237, Estimated correctness of the model 59.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 11062 restraints for refining 5363 atoms. 10104 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2881 (Rfree = 0.000) for 5363 atoms. Found 109 (117 requested) and removed 60 (58 requested) atoms. Cycle 37: After refmac, R = 0.2929 (Rfree = 0.000) for 5406 atoms. Found 107 (118 requested) and removed 69 (59 requested) atoms. Cycle 38: After refmac, R = 0.2954 (Rfree = 0.000) for 5424 atoms. Found 119 (119 requested) and removed 65 (59 requested) atoms. Cycle 39: After refmac, R = 0.2854 (Rfree = 0.000) for 5463 atoms. Found 103 (119 requested) and removed 64 (59 requested) atoms. Cycle 40: After refmac, R = 0.2821 (Rfree = 0.000) for 5481 atoms. Found 98 (120 requested) and removed 66 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.21 2.72 NCS extension: 0 residues added, 5541 seeds are put forward Round 1: 243 peptides, 44 chains. Longest chain 9 peptides. Score 0.331 Round 2: 272 peptides, 44 chains. Longest chain 12 peptides. Score 0.393 Round 3: 262 peptides, 39 chains. Longest chain 19 peptides. Score 0.419 Round 4: 245 peptides, 36 chains. Longest chain 22 peptides. Score 0.412 Round 5: 249 peptides, 36 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 37, Residues 213, Estimated correctness of the model 56.8 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 34670 reflections ( 98.47 % complete ) and 11571 restraints for refining 5516 atoms. 10653 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2939 (Rfree = 0.000) for 5516 atoms. Found 120 (120 requested) and removed 72 (60 requested) atoms. Cycle 42: After refmac, R = 0.2938 (Rfree = 0.000) for 5547 atoms. Found 113 (121 requested) and removed 64 (60 requested) atoms. Cycle 43: After refmac, R = 0.2919 (Rfree = 0.000) for 5578 atoms. Found 102 (122 requested) and removed 73 (61 requested) atoms. Cycle 44: After refmac, R = 0.2587 (Rfree = 0.000) for 5588 atoms. Found 54 (122 requested) and removed 68 (61 requested) atoms. Cycle 45: After refmac, R = 0.2491 (Rfree = 0.000) for 5560 atoms. Found 49 (122 requested) and removed 66 (61 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.16 2.65 NCS extension: 0 residues added, 5575 seeds are put forward Round 1: 203 peptides, 38 chains. Longest chain 10 peptides. Score 0.299 Round 2: 236 peptides, 37 chains. Longest chain 17 peptides. Score 0.383 Round 3: 233 peptides, 40 chains. Longest chain 14 peptides. Score 0.348 Round 4: 253 peptides, 39 chains. Longest chain 14 peptides. Score 0.400 Round 5: 256 peptides, 40 chains. Longest chain 15 peptides. Score 0.397 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 214, Estimated correctness of the model 54.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2o5r-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 34670 reflections ( 98.47 % complete ) and 11618 restraints for refining 5541 atoms. 10801 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2853 (Rfree = 0.000) for 5541 atoms. Found 0 (121 requested) and removed 60 (60 requested) atoms. Cycle 47: After refmac, R = 0.2576 (Rfree = 0.000) for 5478 atoms. Found 0 (120 requested) and removed 60 (60 requested) atoms. Cycle 48: After refmac, R = 0.2539 (Rfree = 0.000) for 5408 atoms. Found 0 (118 requested) and removed 34 (59 requested) atoms. Cycle 49: After refmac, R = 0.2540 (Rfree = 0.000) for 5372 atoms. TimeTaking 83.42