Starting phenix.real_space_refine on Sat Oct 12 23:47:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/10_2024/8s5h_19735_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/10_2024/8s5h_19735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/10_2024/8s5h_19735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/10_2024/8s5h_19735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/10_2024/8s5h_19735_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5h_19735/10_2024/8s5h_19735_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 8 5.49 5 S 176 5.16 5 C 20216 2.51 5 N 5536 2.21 5 O 5960 1.98 5 H 31936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 63840 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 19.56, per 1000 atoms: 0.31 Number of scatterers: 63840 At special positions: 0 Unit cell: (152.985, 150.815, 254.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 176 16.00 P 8 15.00 O 5960 8.00 N 5536 7.00 C 20216 6.00 H 31936 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 3.8 seconds 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7456 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 38 sheets defined 45.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.866A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.714A pdb=" N VAL A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.714A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.882A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS A 481 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.133A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 119 through 133 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 258 through 272 removed outlier: 4.307A pdb=" N ILE B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.712A pdb=" N VAL B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.884A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 398 through 404 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS B 481 " --> pdb=" O GLN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL C 319 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 343 Processing helix chain 'C' and resid 347 through 361 removed outlier: 3.714A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 382 " --> pdb=" O ARG C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 398 through 404 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS C 481 " --> pdb=" O GLN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 148 through 162 Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.866A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 258 through 272 removed outlier: 4.309A pdb=" N ILE D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL D 319 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 343 Processing helix chain 'D' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN D 380 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET D 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 394 Processing helix chain 'D' and resid 398 through 404 Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 430 through 441 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS D 481 " --> pdb=" O GLN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 535 through 548 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 93 through 99 removed outlier: 4.133A pdb=" N LYS E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE E 99 " --> pdb=" O ILE E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 244 Processing helix chain 'E' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 316 through 320 removed outlier: 3.714A pdb=" N VAL E 319 " --> pdb=" O ASP E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 343 Processing helix chain 'E' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET E 382 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 394 Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS E 481 " --> pdb=" O GLN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 535 through 548 Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 119 through 133 Processing helix chain 'F' and resid 148 through 162 Processing helix chain 'F' and resid 174 through 184 removed outlier: 3.782A pdb=" N VAL F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS F 232 " --> pdb=" O ASN F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'F' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL F 319 " --> pdb=" O ASP F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 343 Processing helix chain 'F' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN F 380 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET F 382 " --> pdb=" O ARG F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 394 Processing helix chain 'F' and resid 398 through 404 Processing helix chain 'F' and resid 413 through 417 Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'F' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS F 481 " --> pdb=" O GLN F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 535 through 548 Processing helix chain 'G' and resid 59 through 63 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 119 through 133 Processing helix chain 'G' and resid 148 through 162 Processing helix chain 'G' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 244 Processing helix chain 'G' and resid 258 through 272 removed outlier: 4.309A pdb=" N ILE G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 295 Processing helix chain 'G' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL G 319 " --> pdb=" O ASP G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 343 Processing helix chain 'G' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN G 380 " --> pdb=" O SER G 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET G 382 " --> pdb=" O ARG G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 398 through 404 Processing helix chain 'G' and resid 413 through 417 Processing helix chain 'G' and resid 430 through 441 Processing helix chain 'G' and resid 461 through 470 Processing helix chain 'G' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS G 481 " --> pdb=" O GLN G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 504 Processing helix chain 'G' and resid 535 through 548 Processing helix chain 'H' and resid 59 through 63 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS H 97 " --> pdb=" O ASN H 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE H 99 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 119 through 133 Processing helix chain 'H' and resid 148 through 162 Processing helix chain 'H' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 214 Processing helix chain 'H' and resid 226 through 235 removed outlier: 3.866A pdb=" N HIS H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 244 Processing helix chain 'H' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE H 264 " --> pdb=" O THR H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL H 319 " --> pdb=" O ASP H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 343 Processing helix chain 'H' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 364 No H-bonds generated for 'chain 'H' and resid 362 through 364' Processing helix chain 'H' and resid 377 through 382 removed outlier: 3.882A pdb=" N ASN H 380 " --> pdb=" O SER H 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET H 382 " --> pdb=" O ARG H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 394 Processing helix chain 'H' and resid 398 through 404 Processing helix chain 'H' and resid 413 through 417 Processing helix chain 'H' and resid 430 through 441 Processing helix chain 'H' and resid 461 through 470 Processing helix chain 'H' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS H 481 " --> pdb=" O GLN H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 504 Processing helix chain 'H' and resid 535 through 548 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER A 254 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 251 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 280 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA A 253 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 449 Processing sheet with id=AA4, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.484A pdb=" N LYS A 488 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 512 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 490 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU A 514 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA A 509 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 533 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 511 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER B 254 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 251 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 280 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA B 253 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 Processing sheet with id=AA7, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.794A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS C 488 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 512 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE C 490 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU C 514 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.794A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA C 509 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL C 533 " --> pdb=" O ALA C 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 511 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 449 Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.770A pdb=" N ALA B 509 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 533 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 511 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 490 removed outlier: 7.822A pdb=" N THR C 424 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE B 516 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER C 254 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 251 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL C 280 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA C 253 " --> pdb=" O VAL C 280 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 187 through 191 Processing sheet with id=AB5, first strand: chain 'C' and resid 445 through 449 Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER D 254 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU D 251 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL D 280 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA D 253 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 187 through 191 Processing sheet with id=AB8, first strand: chain 'D' and resid 423 through 425 removed outlier: 3.711A pdb=" N TYR E 518 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 423 through 425 removed outlier: 3.711A pdb=" N TYR E 518 " --> pdb=" O THR D 424 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA E 509 " --> pdb=" O VAL E 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL E 533 " --> pdb=" O ALA E 509 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL E 511 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 445 through 449 Processing sheet with id=AC2, first strand: chain 'D' and resid 488 through 490 removed outlier: 6.769A pdb=" N ALA D 509 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL D 533 " --> pdb=" O ALA D 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D 511 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 488 through 490 removed outlier: 7.790A pdb=" N THR E 424 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE D 516 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER E 254 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU E 251 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL E 280 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA E 253 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 187 through 191 Processing sheet with id=AC6, first strand: chain 'E' and resid 445 through 449 Processing sheet with id=AC7, first strand: chain 'F' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER F 254 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU F 251 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL F 280 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA F 253 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 187 through 191 Processing sheet with id=AC9, first strand: chain 'F' and resid 423 through 425 removed outlier: 3.742A pdb=" N TYR G 518 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 423 through 425 removed outlier: 3.742A pdb=" N TYR G 518 " --> pdb=" O THR F 424 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA G 509 " --> pdb=" O VAL G 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL G 533 " --> pdb=" O ALA G 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL G 511 " --> pdb=" O PHE G 531 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 445 through 449 Processing sheet with id=AD3, first strand: chain 'F' and resid 488 through 490 removed outlier: 6.485A pdb=" N LYS F 488 " --> pdb=" O LEU F 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL F 512 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE F 490 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU F 514 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA F 509 " --> pdb=" O VAL F 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL F 533 " --> pdb=" O ALA F 509 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL F 511 " --> pdb=" O PHE F 531 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 488 through 490 removed outlier: 6.485A pdb=" N LYS F 488 " --> pdb=" O LEU F 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL F 512 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE F 490 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU F 514 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR G 424 " --> pdb=" O GLU F 514 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE F 516 " --> pdb=" O THR G 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER G 254 " --> pdb=" O ILE G 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU G 251 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL G 280 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA G 253 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 187 through 191 Processing sheet with id=AD7, first strand: chain 'G' and resid 445 through 449 Processing sheet with id=AD8, first strand: chain 'H' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER H 254 " --> pdb=" O ILE H 373 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU H 251 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL H 280 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA H 253 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 187 through 191 Processing sheet with id=AE1, first strand: chain 'H' and resid 445 through 449 Processing sheet with id=AE2, first strand: chain 'H' and resid 488 through 490 removed outlier: 6.484A pdb=" N LYS H 488 " --> pdb=" O LEU H 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL H 512 " --> pdb=" O LYS H 488 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE H 490 " --> pdb=" O VAL H 512 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU H 514 " --> pdb=" O ILE H 490 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA H 509 " --> pdb=" O VAL H 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL H 533 " --> pdb=" O ALA H 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL H 511 " --> pdb=" O PHE H 531 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.62 Time building geometry restraints manager: 16.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 31728 1.08 - 1.32: 5592 1.32 - 1.55: 26872 1.55 - 1.79: 104 1.79 - 2.03: 208 Bond restraints: 64504 Sorted by residual: bond pdb=" C4' LLP B 119 " pdb="H4'1 LLP B 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C4' LLP E 119 " pdb="H4'1 LLP E 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C4' LLP D 119 " pdb="H4'1 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" C4' LLP H 119 " pdb="H4'1 LLP H 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" C6 LLP E 119 " pdb=" H6 LLP E 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 64499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 116579 2.86 - 5.71: 462 5.71 - 8.57: 23 8.57 - 11.42: 8 11.42 - 14.28: 8 Bond angle restraints: 117080 Sorted by residual: angle pdb=" O LLP A 119 " pdb=" C LLP A 119 " pdb=" N ASP A 120 " ideal model delta sigma weight residual 123.00 108.72 14.28 1.60e+00 3.91e-01 7.97e+01 angle pdb=" O LLP F 119 " pdb=" C LLP F 119 " pdb=" N ASP F 120 " ideal model delta sigma weight residual 123.00 108.73 14.27 1.60e+00 3.91e-01 7.95e+01 angle pdb=" O LLP E 119 " pdb=" C LLP E 119 " pdb=" N ASP E 120 " ideal model delta sigma weight residual 123.00 108.74 14.26 1.60e+00 3.91e-01 7.94e+01 angle pdb=" O LLP C 119 " pdb=" C LLP C 119 " pdb=" N ASP C 120 " ideal model delta sigma weight residual 123.00 108.75 14.25 1.60e+00 3.91e-01 7.94e+01 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 108.76 14.24 1.60e+00 3.91e-01 7.92e+01 ... (remaining 117075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 26533 17.40 - 34.79: 2292 34.79 - 52.19: 676 52.19 - 69.58: 291 69.58 - 86.98: 104 Dihedral angle restraints: 29896 sinusoidal: 16800 harmonic: 13096 Sorted by residual: dihedral pdb=" CA GLN G 528 " pdb=" C GLN G 528 " pdb=" N MET G 529 " pdb=" CA MET G 529 " ideal model delta harmonic sigma weight residual 180.00 -144.54 -35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA GLN F 528 " pdb=" C GLN F 528 " pdb=" N MET F 529 " pdb=" CA MET F 529 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA GLN E 528 " pdb=" C GLN E 528 " pdb=" N MET E 529 " pdb=" CA MET E 529 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 ... (remaining 29893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3192 0.029 - 0.057: 1127 0.057 - 0.086: 268 0.086 - 0.114: 291 0.114 - 0.143: 82 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA ILE E 516 " pdb=" N ILE E 516 " pdb=" C ILE E 516 " pdb=" CB ILE E 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE C 516 " pdb=" N ILE C 516 " pdb=" C ILE C 516 " pdb=" CB ILE C 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE A 516 " pdb=" N ILE A 516 " pdb=" C ILE A 516 " pdb=" CB ILE A 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 4957 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP F 119 " -0.073 2.00e-02 2.50e+03 1.35e-01 1.83e+02 pdb=" C LLP F 119 " 0.234 2.00e-02 2.50e+03 pdb=" O LLP F 119 " -0.085 2.00e-02 2.50e+03 pdb=" N ASP F 120 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " -0.073 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C LLP D 119 " 0.234 2.00e-02 2.50e+03 pdb=" O LLP D 119 " -0.085 2.00e-02 2.50e+03 pdb=" N ASP D 120 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP A 119 " 0.073 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C LLP A 119 " -0.234 2.00e-02 2.50e+03 pdb=" O LLP A 119 " 0.085 2.00e-02 2.50e+03 pdb=" N ASP A 120 " 0.076 2.00e-02 2.50e+03 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 4742 2.21 - 2.81: 138196 2.81 - 3.41: 180161 3.41 - 4.00: 237694 4.00 - 4.60: 366196 Nonbonded interactions: 926989 Sorted by model distance: nonbonded pdb=" OE2 GLU E 201 " pdb=" HH TYR F 484 " model vdw 1.616 2.450 nonbonded pdb=" OE2 GLU A 201 " pdb=" HH TYR B 484 " model vdw 1.622 2.450 nonbonded pdb=" OE2 GLU H 304 " pdb=" HZ2 LYS H 384 " model vdw 1.625 2.450 nonbonded pdb=" OE2 GLU G 304 " pdb=" HZ2 LYS G 384 " model vdw 1.626 2.450 nonbonded pdb=" OE2 GLU D 304 " pdb=" HZ2 LYS D 384 " model vdw 1.626 2.450 ... (remaining 926984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.820 Extract box with map and model: 1.860 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 101.460 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32568 Z= 0.246 Angle : 0.655 14.280 44232 Z= 0.347 Chirality : 0.040 0.143 4960 Planarity : 0.006 0.135 5656 Dihedral : 14.756 86.977 12120 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.59 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 4016 helix: 0.95 (0.15), residues: 1432 sheet: 0.11 (0.21), residues: 600 loop : 0.71 (0.15), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 208 HIS 0.006 0.001 HIS A 66 PHE 0.016 0.001 PHE H 531 TYR 0.029 0.002 TYR G 518 ARG 0.005 0.000 ARG E 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7740 (mp10) REVERT: C 126 MET cc_start: 0.8529 (mtp) cc_final: 0.8280 (mtp) REVERT: C 364 LEU cc_start: 0.6855 (mt) cc_final: 0.6461 (mt) REVERT: C 391 MET cc_start: 0.7833 (mmm) cc_final: 0.7560 (mmm) REVERT: F 126 MET cc_start: 0.8601 (mtp) cc_final: 0.8344 (mtp) REVERT: F 391 MET cc_start: 0.7851 (mmm) cc_final: 0.7609 (mmm) REVERT: G 505 MET cc_start: 0.7581 (mmt) cc_final: 0.7366 (mmp) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.9946 time to fit residues: 557.7524 Evaluate side-chains 240 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 233 optimal weight: 0.6980 chunk 363 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32568 Z= 0.188 Angle : 0.556 7.534 44232 Z= 0.285 Chirality : 0.043 0.158 4960 Planarity : 0.004 0.036 5656 Dihedral : 7.893 89.265 4448 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.53 % Allowed : 11.24 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 4016 helix: 0.72 (0.14), residues: 1512 sheet: 0.22 (0.20), residues: 608 loop : 0.43 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 208 HIS 0.003 0.001 HIS A 507 PHE 0.011 0.001 PHE E 531 TYR 0.020 0.001 TYR B 518 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 259 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 474 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7629 (mp10) REVERT: B 540 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8570 (tt) REVERT: C 126 MET cc_start: 0.8557 (mtp) cc_final: 0.8343 (mtp) REVERT: C 540 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8358 (tp) REVERT: D 429 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6454 (tt) REVERT: D 540 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8526 (tt) REVERT: E 429 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6486 (tt) REVERT: E 540 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8476 (tt) REVERT: F 126 MET cc_start: 0.8532 (mtp) cc_final: 0.8321 (mtp) REVERT: F 540 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8323 (tp) REVERT: G 540 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8619 (tt) outliers start: 18 outliers final: 3 residues processed: 270 average time/residue: 0.8646 time to fit residues: 374.5539 Evaluate side-chains 225 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain H residue 241 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 393 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 360 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 HIS F 489 GLN G 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 32568 Z= 0.357 Angle : 0.615 7.947 44232 Z= 0.322 Chirality : 0.044 0.171 4960 Planarity : 0.005 0.061 5656 Dihedral : 8.083 88.134 4448 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.24 % Rotamer: Outliers : 1.43 % Allowed : 12.27 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 4016 helix: 0.51 (0.14), residues: 1504 sheet: -0.10 (0.20), residues: 608 loop : 0.29 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 208 HIS 0.006 0.001 HIS H 507 PHE 0.017 0.002 PHE D 332 TYR 0.016 0.002 TYR F 163 ARG 0.004 0.001 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 209 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6638 (t0) REVERT: B 474 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7662 (mp10) REVERT: B 540 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8538 (tt) REVERT: C 126 MET cc_start: 0.8647 (mtp) cc_final: 0.8445 (mtp) REVERT: C 302 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: C 391 MET cc_start: 0.8177 (mmm) cc_final: 0.7903 (mmm) REVERT: C 540 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8398 (tp) REVERT: D 302 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: D 429 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6998 (tt) REVERT: D 540 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8678 (tt) REVERT: E 302 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: E 429 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6991 (tt) REVERT: E 540 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8604 (tt) REVERT: F 126 MET cc_start: 0.8623 (mtp) cc_final: 0.8422 (mtp) REVERT: F 302 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: F 391 MET cc_start: 0.8195 (mmm) cc_final: 0.7927 (mmm) REVERT: F 540 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8532 (tp) REVERT: G 540 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8517 (tt) REVERT: H 129 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7071 (t0) outliers start: 49 outliers final: 20 residues processed: 248 average time/residue: 0.7715 time to fit residues: 317.6191 Evaluate side-chains 220 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 365 optimal weight: 3.9990 chunk 386 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 346 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 32568 Z= 0.298 Angle : 0.569 7.182 44232 Z= 0.293 Chirality : 0.043 0.163 4960 Planarity : 0.004 0.045 5656 Dihedral : 7.958 87.872 4448 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.29 % Allowed : 13.23 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 4016 helix: 0.52 (0.14), residues: 1504 sheet: -0.22 (0.20), residues: 616 loop : 0.29 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 208 HIS 0.006 0.001 HIS D 66 PHE 0.016 0.002 PHE D 385 TYR 0.013 0.002 TYR H 163 ARG 0.004 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7775 (ptm) cc_final: 0.7550 (ptt) REVERT: B 474 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7684 (mp-120) REVERT: C 302 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: C 531 PHE cc_start: 0.7056 (m-10) cc_final: 0.6665 (m-80) REVERT: C 540 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8379 (tp) REVERT: D 429 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6858 (tt) REVERT: D 464 MET cc_start: 0.7561 (mtm) cc_final: 0.7334 (mtm) REVERT: D 540 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8633 (tt) REVERT: E 173 MET cc_start: 0.8622 (mmt) cc_final: 0.8268 (mmt) REVERT: E 429 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7023 (tt) REVERT: E 464 MET cc_start: 0.7605 (mtm) cc_final: 0.7368 (mtm) REVERT: E 540 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8692 (tt) REVERT: F 302 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: F 540 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8460 (tp) outliers start: 44 outliers final: 30 residues processed: 235 average time/residue: 0.7936 time to fit residues: 305.8380 Evaluate side-chains 225 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 329 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 32568 Z= 0.324 Angle : 0.578 6.868 44232 Z= 0.299 Chirality : 0.043 0.166 4960 Planarity : 0.004 0.043 5656 Dihedral : 7.985 87.925 4448 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.81 % Allowed : 13.58 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.13), residues: 4016 helix: 0.44 (0.14), residues: 1504 sheet: -0.32 (0.20), residues: 616 loop : 0.24 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 410 HIS 0.006 0.001 HIS D 66 PHE 0.016 0.002 PHE D 385 TYR 0.014 0.001 TYR H 163 ARG 0.008 0.000 ARG F 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7620 (mp10) REVERT: C 173 MET cc_start: 0.8524 (mmt) cc_final: 0.8317 (mmt) REVERT: C 302 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: C 531 PHE cc_start: 0.7156 (m-10) cc_final: 0.6731 (m-80) REVERT: C 540 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8587 (tp) REVERT: D 302 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: D 429 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7374 (tt) REVERT: D 540 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8676 (tt) REVERT: E 173 MET cc_start: 0.8585 (mmt) cc_final: 0.8243 (mmt) REVERT: E 302 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: E 540 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8570 (tt) REVERT: F 302 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: F 531 PHE cc_start: 0.7297 (m-10) cc_final: 0.6922 (m-80) REVERT: F 540 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8463 (tp) REVERT: G 451 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: G 505 MET cc_start: 0.8311 (mmt) cc_final: 0.8049 (mmt) REVERT: H 129 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7016 (t0) outliers start: 62 outliers final: 39 residues processed: 248 average time/residue: 0.8518 time to fit residues: 344.3198 Evaluate side-chains 241 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 95 optimal weight: 0.0970 chunk 387 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 chunk 128 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 overall best weight: 2.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32568 Z= 0.205 Angle : 0.522 6.643 44232 Z= 0.262 Chirality : 0.042 0.152 4960 Planarity : 0.004 0.042 5656 Dihedral : 7.805 89.287 4448 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.17 % Allowed : 14.46 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 4016 helix: 0.68 (0.14), residues: 1504 sheet: -0.23 (0.20), residues: 616 loop : 0.38 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 408 HIS 0.007 0.001 HIS D 66 PHE 0.011 0.001 PHE D 332 TYR 0.009 0.001 TYR D 518 ARG 0.006 0.000 ARG F 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7597 (mp10) REVERT: C 531 PHE cc_start: 0.7136 (m-10) cc_final: 0.6778 (m-80) REVERT: C 540 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8483 (tp) REVERT: D 302 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: D 540 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8653 (tt) REVERT: E 171 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7844 (tm-30) REVERT: E 302 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: E 464 MET cc_start: 0.7565 (mtm) cc_final: 0.7350 (mtm) REVERT: E 540 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8629 (tt) REVERT: F 531 PHE cc_start: 0.7244 (m-10) cc_final: 0.6846 (m-80) REVERT: F 540 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8349 (tp) REVERT: G 451 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5872 (mp0) outliers start: 40 outliers final: 31 residues processed: 233 average time/residue: 0.8122 time to fit residues: 311.0831 Evaluate side-chains 231 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 325 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 385 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 216 ASN E 216 ASN E 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 32568 Z= 0.427 Angle : 0.630 7.143 44232 Z= 0.329 Chirality : 0.045 0.182 4960 Planarity : 0.005 0.046 5656 Dihedral : 8.078 89.015 4448 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.99 % Allowed : 14.40 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4016 helix: 0.26 (0.13), residues: 1504 sheet: -0.24 (0.22), residues: 552 loop : 0.05 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 208 HIS 0.008 0.001 HIS D 66 PHE 0.026 0.002 PHE C 385 TYR 0.015 0.002 TYR H 163 ARG 0.007 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 190 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8611 (p) REVERT: B 474 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7719 (mp10) REVERT: C 302 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: C 314 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9166 (p) REVERT: C 434 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8752 (p) REVERT: C 531 PHE cc_start: 0.7231 (m-10) cc_final: 0.6840 (m-80) REVERT: C 540 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8477 (tp) REVERT: D 216 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7621 (t0) REVERT: D 302 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: D 391 MET cc_start: 0.8022 (mmt) cc_final: 0.7741 (mmt) REVERT: D 540 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (tt) REVERT: E 216 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7577 (t0) REVERT: E 302 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: F 302 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: F 531 PHE cc_start: 0.7399 (m-10) cc_final: 0.7029 (m-80) REVERT: F 540 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8554 (tp) REVERT: G 505 MET cc_start: 0.8361 (mmt) cc_final: 0.8103 (mmt) REVERT: H 314 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8588 (p) outliers start: 68 outliers final: 40 residues processed: 249 average time/residue: 0.7790 time to fit residues: 323.4848 Evaluate side-chains 238 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 185 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 32568 Z= 0.230 Angle : 0.544 6.413 44232 Z= 0.275 Chirality : 0.042 0.158 4960 Planarity : 0.004 0.042 5656 Dihedral : 7.879 89.494 4448 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.29 % Allowed : 15.19 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 4016 helix: 0.53 (0.14), residues: 1504 sheet: -0.22 (0.21), residues: 560 loop : 0.22 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 208 HIS 0.008 0.001 HIS D 66 PHE 0.013 0.001 PHE D 443 TYR 0.016 0.001 TYR F 518 ARG 0.005 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 3.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6805 (t0) REVERT: A 314 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 474 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7687 (mp10) REVERT: C 302 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: C 314 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9146 (p) REVERT: C 434 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8769 (p) REVERT: C 464 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7224 (ttm) REVERT: C 531 PHE cc_start: 0.7199 (m-10) cc_final: 0.6781 (m-80) REVERT: C 540 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8468 (tp) REVERT: D 302 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: D 328 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7401 (p0) REVERT: D 540 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8648 (tt) REVERT: E 302 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: E 328 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7361 (p0) REVERT: F 302 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: F 314 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9135 (p) REVERT: F 531 PHE cc_start: 0.7403 (m-10) cc_final: 0.7010 (m-80) REVERT: F 540 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8475 (tp) REVERT: G 505 MET cc_start: 0.8296 (mmt) cc_final: 0.8046 (mmt) REVERT: H 314 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8551 (p) outliers start: 44 outliers final: 25 residues processed: 231 average time/residue: 0.8354 time to fit residues: 319.9459 Evaluate side-chains 230 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 336 optimal weight: 0.9980 chunk 359 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 358 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 32568 Z= 0.250 Angle : 0.541 5.932 44232 Z= 0.273 Chirality : 0.042 0.159 4960 Planarity : 0.004 0.041 5656 Dihedral : 7.830 89.996 4448 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.37 % Allowed : 14.89 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 4016 helix: 0.63 (0.14), residues: 1504 sheet: -0.20 (0.21), residues: 560 loop : 0.27 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 208 HIS 0.009 0.001 HIS D 66 PHE 0.017 0.001 PHE E 531 TYR 0.014 0.001 TYR F 518 ARG 0.004 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6789 (t0) REVERT: A 314 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8719 (p) REVERT: B 474 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7748 (mp10) REVERT: C 302 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: C 314 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9132 (p) REVERT: C 434 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8764 (p) REVERT: C 531 PHE cc_start: 0.7162 (m-10) cc_final: 0.6737 (m-80) REVERT: C 540 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8469 (tp) REVERT: D 302 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: D 328 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7425 (p0) REVERT: D 540 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8647 (tt) REVERT: E 173 MET cc_start: 0.8337 (mmt) cc_final: 0.8105 (mmt) REVERT: E 302 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: E 328 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7403 (p0) REVERT: F 302 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: F 314 VAL cc_start: 0.9377 (OUTLIER) cc_final: 0.9122 (p) REVERT: F 434 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8806 (p) REVERT: F 540 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8452 (tp) REVERT: G 505 MET cc_start: 0.8302 (mmt) cc_final: 0.8030 (mmt) REVERT: H 314 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8603 (p) outliers start: 47 outliers final: 28 residues processed: 237 average time/residue: 0.7661 time to fit residues: 302.9632 Evaluate side-chains 233 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 189 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 0.5980 chunk 379 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 398 optimal weight: 8.9990 chunk 366 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32568 Z= 0.297 Angle : 0.564 6.209 44232 Z= 0.287 Chirality : 0.043 0.163 4960 Planarity : 0.004 0.042 5656 Dihedral : 7.887 89.776 4448 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.43 % Allowed : 15.07 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 4016 helix: 0.53 (0.14), residues: 1504 sheet: -0.21 (0.22), residues: 560 loop : 0.24 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 208 HIS 0.007 0.001 HIS D 66 PHE 0.026 0.002 PHE E 531 TYR 0.019 0.001 TYR F 518 ARG 0.005 0.000 ARG C 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 4.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6580 (t0) REVERT: A 314 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 474 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7771 (mp10) REVERT: C 302 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: C 314 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9146 (p) REVERT: C 434 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8760 (p) REVERT: C 531 PHE cc_start: 0.7285 (m-10) cc_final: 0.6941 (m-80) REVERT: C 540 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8484 (tp) REVERT: D 302 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: D 540 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8665 (tt) REVERT: E 302 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: F 302 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: F 314 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9146 (p) REVERT: F 434 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8793 (p) REVERT: F 540 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8411 (tp) REVERT: G 505 MET cc_start: 0.8333 (mmt) cc_final: 0.8067 (mmt) REVERT: H 314 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8607 (p) outliers start: 49 outliers final: 31 residues processed: 240 average time/residue: 0.8164 time to fit residues: 327.8647 Evaluate side-chains 237 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 0.9980 chunk 338 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.110462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085463 restraints weight = 228248.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087272 restraints weight = 128972.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088093 restraints weight = 112001.083| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32568 Z= 0.296 Angle : 0.563 6.531 44232 Z= 0.286 Chirality : 0.043 0.164 4960 Planarity : 0.004 0.042 5656 Dihedral : 7.867 87.931 4448 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.49 % Allowed : 15.10 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 4016 helix: 0.54 (0.14), residues: 1504 sheet: -0.16 (0.22), residues: 552 loop : 0.21 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 208 HIS 0.008 0.001 HIS D 66 PHE 0.015 0.002 PHE C 385 TYR 0.010 0.001 TYR H 163 ARG 0.004 0.000 ARG C 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8249.19 seconds wall clock time: 145 minutes 21.78 seconds (8721.78 seconds total)