Starting phenix.real_space_refine on Fri Mar 15 17:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/03_2024/6hco_0196_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/03_2024/6hco_0196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/03_2024/6hco_0196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/03_2024/6hco_0196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/03_2024/6hco_0196_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hco_0196/03_2024/6hco_0196_neut_updated.pdb" } resolution = 3.58 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= 0.004 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 7960 2.51 5 N 2032 2.21 5 O 2277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12338 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "B" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'FY5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.54 Number of scatterers: 12338 At special positions: 0 Unit cell: (101.5, 93.38, 142.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2277 8.00 N 2032 7.00 C 7960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 12 sheets defined 37.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.198A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.768A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.731A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.862A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.620A pdb=" N LEU A 274 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 277 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 278 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 340 through 352 removed outlier: 3.729A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.665A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 removed outlier: 4.075A pdb=" N ILE A 400 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 401 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 404 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 405 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 408 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 409 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 412 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.731A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 476 removed outlier: 4.015A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 No H-bonds generated for 'chain 'A' and resid 480 through 483' Processing helix chain 'A' and resid 485 through 497 removed outlier: 4.222A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.574A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 removed outlier: 3.569A pdb=" N LEU A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.546A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.808A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 154 through 162 removed outlier: 4.266A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.742A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 231 removed outlier: 3.708A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.861A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 removed outlier: 3.608A pdb=" N LEU B 274 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 277 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 278 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 340 through 352 removed outlier: 3.754A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 380 through 389 removed outlier: 3.668A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 4.115A pdb=" N ILE B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 404 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 405 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 408 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE B 409 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 439 Processing helix chain 'B' and resid 441 through 450 removed outlier: 3.682A pdb=" N PHE B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 449 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 476 removed outlier: 4.017A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 No H-bonds generated for 'chain 'B' and resid 480 through 483' Processing helix chain 'B' and resid 485 through 497 removed outlier: 4.226A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 3.565A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.587A pdb=" N LEU B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 546 " --> pdb=" O THR B 542 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.549A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.835A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.629A pdb=" N GLY A 69 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.090A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N GLY A 80 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.590A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.158A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.653A pdb=" N PHE D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.349A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 34 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 19 through 24 removed outlier: 3.590A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 88 through 90 removed outlier: 6.158A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 19 through 23 removed outlier: 3.654A pdb=" N PHE F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.348A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 34 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.648A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 263 through 269 removed outlier: 6.089A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1095 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: 3.58 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1935 1.30 - 1.43: 3507 1.43 - 1.56: 7058 1.56 - 1.68: 7 1.68 - 1.81: 106 Bond restraints: 12613 Sorted by residual: bond pdb=" C02 FY5 A1003 " pdb=" C10 FY5 A1003 " ideal model delta sigma weight residual 1.518 1.328 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" C04 FY5 A1003 " pdb=" C05 FY5 A1003 " ideal model delta sigma weight residual 1.527 1.667 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C07 FY5 A1003 " pdb=" C08 FY5 A1003 " ideal model delta sigma weight residual 1.527 1.397 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C02 FY5 A1003 " pdb=" C07 FY5 A1003 " ideal model delta sigma weight residual 1.533 1.650 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" N ASN B 436 " pdb=" CA ASN B 436 " ideal model delta sigma weight residual 1.459 1.398 0.061 1.17e-02 7.31e+03 2.72e+01 ... (remaining 12608 not shown) Histogram of bond angle deviations from ideal: 96.72 - 104.19: 177 104.19 - 111.66: 5660 111.66 - 119.13: 4528 119.13 - 126.60: 6565 126.60 - 134.07: 165 Bond angle restraints: 17095 Sorted by residual: angle pdb=" N ASN B 436 " pdb=" CA ASN B 436 " pdb=" C ASN B 436 " ideal model delta sigma weight residual 110.97 102.48 8.49 1.09e+00 8.42e-01 6.07e+01 angle pdb=" N ASN A 436 " pdb=" CA ASN A 436 " pdb=" C ASN A 436 " ideal model delta sigma weight residual 110.97 102.58 8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" C THR A 435 " pdb=" N ASN A 436 " pdb=" CA ASN A 436 " ideal model delta sigma weight residual 120.65 110.74 9.91 1.32e+00 5.74e-01 5.63e+01 angle pdb=" C THR B 435 " pdb=" N ASN B 436 " pdb=" CA ASN B 436 " ideal model delta sigma weight residual 120.65 110.91 9.74 1.32e+00 5.74e-01 5.45e+01 angle pdb=" O22 FY5 A1003 " pdb=" S21 FY5 A1003 " pdb=" O23 FY5 A1003 " ideal model delta sigma weight residual 115.34 97.62 17.72 3.00e+00 1.11e-01 3.49e+01 ... (remaining 17090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7186 17.89 - 35.78: 251 35.78 - 53.67: 52 53.67 - 71.56: 4 71.56 - 89.44: 9 Dihedral angle restraints: 7502 sinusoidal: 2986 harmonic: 4516 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 16.14 76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CA GLY F 43 " pdb=" C GLY F 43 " pdb=" N LYS F 44 " pdb=" CA LYS F 44 " ideal model delta harmonic sigma weight residual -180.00 -149.39 -30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA GLY D 43 " pdb=" C GLY D 43 " pdb=" N LYS D 44 " pdb=" CA LYS D 44 " ideal model delta harmonic sigma weight residual -180.00 -149.40 -30.60 0 5.00e+00 4.00e-02 3.75e+01 ... (remaining 7499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1279 0.053 - 0.106: 538 0.106 - 0.159: 120 0.159 - 0.212: 15 0.212 - 0.265: 6 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C05 FY5 A1003 " pdb=" C04 FY5 A1003 " pdb=" C06 FY5 A1003 " pdb=" C15 FY5 A1003 " both_signs ideal model delta sigma weight residual False 2.38 2.62 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1955 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 63 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE B 63 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE B 63 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 64 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 63 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE A 63 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE A 63 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 64 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 98 " 0.006 2.00e-02 2.50e+03 1.94e-02 6.57e+00 pdb=" CG PHE E 98 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 98 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE E 98 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE E 98 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE E 98 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 98 " -0.005 2.00e-02 2.50e+03 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 219 2.65 - 3.21: 11413 3.21 - 3.77: 19431 3.77 - 4.34: 27032 4.34 - 4.90: 43430 Nonbonded interactions: 101525 Sorted by model distance: nonbonded pdb=" O PHE B 431 " pdb=" CG2 THR B 435 " model vdw 2.082 3.460 nonbonded pdb=" O PHE A 431 " pdb=" CG2 THR A 435 " model vdw 2.108 3.460 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.185 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.188 2.440 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.267 2.440 ... (remaining 101520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 654) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = 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: 3.610 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: 0.010 Extract box with map and model: 10.780 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 35.540 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.009 0.190 12613 Z= 0.596 Angle : 1.046 17.718 17095 Z= 0.545 Chirality : 0.058 0.265 1958 Planarity : 0.007 0.057 2130 Dihedral : 10.572 89.444 4597 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.45 % Allowed : 4.02 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.59 (0.17), residues: 1552 helix: -3.41 (0.13), residues: 578 sheet: -2.92 (0.27), residues: 274 loop : -2.60 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP E 96 HIS 0.015 0.004 HIS A 583 PHE 0.040 0.004 PHE E 98 TYR 0.028 0.004 TYR B 570 ARG 0.011 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 249 time to evaluate : 1.439 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: A 206 ILE cc_start: 0.8807 (mt) cc_final: 0.8583 (mm) REVERT: A 207 LEU cc_start: 0.9286 (mp) cc_final: 0.8830 (tt) REVERT: A 251 LYS cc_start: 0.7555 (pttt) cc_final: 0.7203 (tptp) REVERT: A 441 SER cc_start: 0.8983 (m) cc_final: 0.8076 (t) REVERT: A 636 MET cc_start: 0.8160 (mtp) cc_final: 0.7728 (mmt) REVERT: F 53 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7871 (t0) outliers start: 6 outliers final: 2 residues processed: 252 average time/residue: 0.2480 time to fit residues: 88.7560 Evaluate side-chains 129 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain B residue 435 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 68 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 425 ASN A 436 ASN A 437 GLN A 583 HIS D 77 ASN F 53 ASN F 77 ASN B 41 ASN B 68 ASN B 116 ASN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 425 ASN B 436 ASN B 437 GLN B 582 GLN B 583 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12613 Z= 0.208 Angle : 0.707 10.648 17095 Z= 0.354 Chirality : 0.044 0.223 1958 Planarity : 0.005 0.053 2130 Dihedral : 6.919 85.527 1821 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.23 % Allowed : 8.71 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.67 (0.20), residues: 1552 helix: -1.19 (0.19), residues: 572 sheet: -2.22 (0.30), residues: 262 loop : -1.99 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 564 HIS 0.003 0.001 HIS A 350 PHE 0.025 0.002 PHE A 250 TYR 0.016 0.002 TYR A 342 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.466 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: A 198 MET cc_start: 0.8405 (mtt) cc_final: 0.8086 (mtm) REVERT: A 206 ILE cc_start: 0.8988 (mt) cc_final: 0.8757 (mm) REVERT: A 207 LEU cc_start: 0.9462 (mp) cc_final: 0.9023 (tp) REVERT: A 251 LYS cc_start: 0.7559 (pttt) cc_final: 0.7358 (pptt) REVERT: A 334 GLU cc_start: 0.8259 (tp30) cc_final: 0.7434 (pp20) REVERT: A 441 SER cc_start: 0.8988 (m) cc_final: 0.8316 (t) REVERT: A 636 MET cc_start: 0.8227 (mtp) cc_final: 0.7750 (mmt) REVERT: B 164 VAL cc_start: 0.9402 (t) cc_final: 0.9171 (m) REVERT: B 228 LEU cc_start: 0.9122 (mt) cc_final: 0.8590 (pp) REVERT: B 446 GLU cc_start: 0.8270 (mp0) cc_final: 0.7964 (mp0) outliers start: 30 outliers final: 14 residues processed: 161 average time/residue: 0.2163 time to fit residues: 52.6194 Evaluate side-chains 132 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 635 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 0.0870 chunk 112 optimal weight: 5.9990 overall best weight: 2.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 12613 Z= 0.293 Angle : 0.705 12.270 17095 Z= 0.349 Chirality : 0.044 0.202 1958 Planarity : 0.004 0.042 2130 Dihedral : 6.351 89.606 1817 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.27 % Allowed : 9.67 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.22), residues: 1552 helix: -0.35 (0.21), residues: 588 sheet: -1.78 (0.31), residues: 272 loop : -1.43 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 624 HIS 0.004 0.001 HIS A 630 PHE 0.026 0.002 PHE A 578 TYR 0.013 0.002 TYR A 570 ARG 0.004 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8041 (mmt) cc_final: 0.7716 (mmp) REVERT: A 198 MET cc_start: 0.8481 (mtt) cc_final: 0.8167 (mtm) REVERT: A 206 ILE cc_start: 0.9061 (mt) cc_final: 0.8849 (mm) REVERT: A 207 LEU cc_start: 0.9530 (mp) cc_final: 0.9039 (tt) REVERT: A 228 LEU cc_start: 0.9030 (mt) cc_final: 0.8295 (pp) REVERT: A 251 LYS cc_start: 0.7587 (pttt) cc_final: 0.7376 (pptt) REVERT: A 441 SER cc_start: 0.9137 (m) cc_final: 0.8496 (t) REVERT: A 486 SER cc_start: 0.8580 (m) cc_final: 0.7880 (t) REVERT: A 540 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9233 (mt) REVERT: E 70 ASP cc_start: 0.8311 (m-30) cc_final: 0.7434 (m-30) REVERT: B 71 MET cc_start: 0.8235 (mmm) cc_final: 0.7765 (mmp) REVERT: B 446 GLU cc_start: 0.8392 (mp0) cc_final: 0.8105 (mp0) REVERT: B 486 SER cc_start: 0.8494 (m) cc_final: 0.7549 (t) REVERT: B 540 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9137 (mt) outliers start: 44 outliers final: 25 residues processed: 157 average time/residue: 0.2144 time to fit residues: 51.8474 Evaluate side-chains 134 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 642 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 72 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 148 optimal weight: 0.0980 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12613 Z= 0.181 Angle : 0.621 11.716 17095 Z= 0.302 Chirality : 0.041 0.178 1958 Planarity : 0.004 0.039 2130 Dihedral : 5.915 88.009 1817 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.68 % Allowed : 11.53 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.22), residues: 1552 helix: -0.09 (0.21), residues: 610 sheet: -1.54 (0.31), residues: 274 loop : -1.44 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 624 HIS 0.004 0.001 HIS B 457 PHE 0.020 0.001 PHE A 578 TYR 0.011 0.001 TYR E 91 ARG 0.004 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8004 (mmt) cc_final: 0.7748 (mmp) REVERT: A 206 ILE cc_start: 0.9047 (mt) cc_final: 0.8846 (mm) REVERT: A 207 LEU cc_start: 0.9532 (mp) cc_final: 0.9058 (tt) REVERT: A 228 LEU cc_start: 0.9006 (mt) cc_final: 0.8317 (pp) REVERT: A 334 GLU cc_start: 0.8272 (tp30) cc_final: 0.7503 (pp20) REVERT: A 486 SER cc_start: 0.8539 (m) cc_final: 0.8169 (t) REVERT: A 540 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9201 (mp) REVERT: F 91 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7525 (t) REVERT: B 71 MET cc_start: 0.8193 (mmm) cc_final: 0.7733 (mmp) REVERT: B 164 VAL cc_start: 0.9356 (t) cc_final: 0.9141 (m) REVERT: B 446 GLU cc_start: 0.8431 (mp0) cc_final: 0.8195 (mp0) REVERT: B 486 SER cc_start: 0.8479 (m) cc_final: 0.8047 (t) outliers start: 36 outliers final: 22 residues processed: 143 average time/residue: 0.1927 time to fit residues: 43.4044 Evaluate side-chains 126 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 582 GLN A 589 GLN C 37 GLN E 37 GLN F 40 GLN F 111 GLN B 589 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 12613 Z= 0.561 Angle : 0.867 11.117 17095 Z= 0.434 Chirality : 0.047 0.181 1958 Planarity : 0.005 0.042 2130 Dihedral : 6.687 85.311 1817 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.42 % Allowed : 12.43 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.22), residues: 1552 helix: -0.18 (0.21), residues: 584 sheet: -1.42 (0.31), residues: 274 loop : -1.22 (0.27), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 624 HIS 0.007 0.002 HIS A 583 PHE 0.032 0.003 PHE F 79 TYR 0.032 0.003 TYR A 494 ARG 0.009 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 87 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8052 (mmt) cc_final: 0.7792 (mmp) REVERT: A 207 LEU cc_start: 0.9517 (mp) cc_final: 0.9159 (tt) REVERT: A 486 SER cc_start: 0.8835 (m) cc_final: 0.8455 (t) REVERT: A 540 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9263 (mm) REVERT: B 71 MET cc_start: 0.8282 (mmm) cc_final: 0.7862 (mmp) REVERT: B 342 TYR cc_start: 0.8143 (t80) cc_final: 0.7733 (t80) REVERT: B 486 SER cc_start: 0.8661 (m) cc_final: 0.8346 (t) outliers start: 46 outliers final: 38 residues processed: 124 average time/residue: 0.2151 time to fit residues: 42.7120 Evaluate side-chains 118 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 79 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0980 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.0170 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN C 37 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12613 Z= 0.176 Angle : 0.646 10.330 17095 Z= 0.315 Chirality : 0.042 0.224 1958 Planarity : 0.004 0.041 2130 Dihedral : 6.042 86.863 1817 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.83 % Allowed : 13.84 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.22), residues: 1552 helix: 0.20 (0.21), residues: 594 sheet: -1.11 (0.31), residues: 274 loop : -1.17 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 624 HIS 0.003 0.001 HIS B 267 PHE 0.024 0.002 PHE A 578 TYR 0.011 0.001 TYR E 91 ARG 0.006 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 71 MET cc_start: 0.8014 (mmt) cc_final: 0.7718 (mmp) REVERT: A 207 LEU cc_start: 0.9524 (mp) cc_final: 0.9130 (tt) REVERT: A 334 GLU cc_start: 0.8387 (tp30) cc_final: 0.7704 (pp20) REVERT: A 486 SER cc_start: 0.8664 (m) cc_final: 0.8381 (t) REVERT: B 71 MET cc_start: 0.8206 (mmm) cc_final: 0.7807 (mmp) REVERT: B 228 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8522 (pp) REVERT: B 486 SER cc_start: 0.8422 (m) cc_final: 0.8117 (t) outliers start: 38 outliers final: 24 residues processed: 117 average time/residue: 0.1914 time to fit residues: 36.3473 Evaluate side-chains 105 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12613 Z= 0.402 Angle : 0.734 10.665 17095 Z= 0.365 Chirality : 0.045 0.340 1958 Planarity : 0.004 0.046 2130 Dihedral : 6.210 85.993 1817 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.90 % Allowed : 13.32 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.22), residues: 1552 helix: 0.21 (0.21), residues: 590 sheet: -1.06 (0.31), residues: 274 loop : -1.11 (0.27), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 624 HIS 0.004 0.001 HIS A 267 PHE 0.023 0.002 PHE F 79 TYR 0.025 0.002 TYR A 494 ARG 0.008 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 77 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7975 (mmt) cc_final: 0.7718 (mmp) REVERT: A 334 GLU cc_start: 0.8441 (tp30) cc_final: 0.7781 (pp20) REVERT: A 486 SER cc_start: 0.8804 (m) cc_final: 0.8470 (t) REVERT: A 540 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9231 (mp) REVERT: B 71 MET cc_start: 0.8267 (mmm) cc_final: 0.7871 (mmp) REVERT: B 486 SER cc_start: 0.8581 (m) cc_final: 0.8237 (t) outliers start: 39 outliers final: 31 residues processed: 104 average time/residue: 0.1931 time to fit residues: 32.5945 Evaluate side-chains 106 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12613 Z= 0.215 Angle : 0.645 11.008 17095 Z= 0.317 Chirality : 0.043 0.302 1958 Planarity : 0.004 0.041 2130 Dihedral : 5.951 89.386 1817 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.27 % Allowed : 13.47 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.22), residues: 1552 helix: 0.44 (0.21), residues: 596 sheet: -0.86 (0.31), residues: 274 loop : -1.19 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 624 HIS 0.003 0.001 HIS B 267 PHE 0.020 0.001 PHE A 578 TYR 0.011 0.001 TYR D 95 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 81 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7949 (mmt) cc_final: 0.7706 (mmp) REVERT: A 334 GLU cc_start: 0.8427 (tp30) cc_final: 0.7811 (pp20) REVERT: A 486 SER cc_start: 0.8736 (m) cc_final: 0.8393 (t) REVERT: A 540 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9166 (mt) REVERT: D 49 MET cc_start: 0.7862 (mmt) cc_final: 0.7181 (mmt) REVERT: B 71 MET cc_start: 0.8230 (mmm) cc_final: 0.7844 (mmp) REVERT: B 228 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8550 (pp) REVERT: B 486 SER cc_start: 0.8626 (m) cc_final: 0.8418 (t) outliers start: 44 outliers final: 31 residues processed: 112 average time/residue: 0.1932 time to fit residues: 34.5290 Evaluate side-chains 111 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 130 optimal weight: 0.0270 chunk 137 optimal weight: 0.0770 chunk 90 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12613 Z= 0.154 Angle : 0.606 11.320 17095 Z= 0.294 Chirality : 0.042 0.309 1958 Planarity : 0.003 0.040 2130 Dihedral : 5.565 87.572 1817 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.16 % Allowed : 14.96 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.22), residues: 1552 helix: 0.73 (0.21), residues: 596 sheet: -0.60 (0.32), residues: 274 loop : -1.13 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 48 HIS 0.002 0.001 HIS B 267 PHE 0.016 0.001 PHE A 578 TYR 0.009 0.001 TYR A 459 ARG 0.006 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8373 (tp30) cc_final: 0.7801 (pp20) REVERT: A 486 SER cc_start: 0.8656 (m) cc_final: 0.8335 (t) REVERT: A 540 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9214 (mp) REVERT: D 49 MET cc_start: 0.7826 (mmt) cc_final: 0.7385 (mmt) REVERT: B 71 MET cc_start: 0.8207 (mmm) cc_final: 0.7836 (mmp) REVERT: B 228 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 486 SER cc_start: 0.8536 (m) cc_final: 0.8315 (t) REVERT: B 548 MET cc_start: 0.9164 (mtt) cc_final: 0.8959 (mtt) outliers start: 29 outliers final: 21 residues processed: 109 average time/residue: 0.1840 time to fit residues: 32.6157 Evaluate side-chains 101 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 0.5980 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 0.0020 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12613 Z= 0.153 Angle : 0.624 11.605 17095 Z= 0.296 Chirality : 0.041 0.294 1958 Planarity : 0.003 0.041 2130 Dihedral : 5.432 85.448 1817 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.79 % Allowed : 15.03 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.22), residues: 1552 helix: 0.83 (0.21), residues: 602 sheet: -0.50 (0.33), residues: 276 loop : -1.18 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 35 HIS 0.002 0.000 HIS B 267 PHE 0.015 0.001 PHE A 578 TYR 0.009 0.001 TYR C 91 ARG 0.006 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8372 (tp30) cc_final: 0.7812 (pp20) REVERT: A 486 SER cc_start: 0.8661 (m) cc_final: 0.8328 (t) REVERT: D 49 MET cc_start: 0.7756 (mmt) cc_final: 0.7273 (mmt) REVERT: B 71 MET cc_start: 0.8135 (mmm) cc_final: 0.7831 (mmp) REVERT: B 228 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8548 (pp) outliers start: 24 outliers final: 18 residues processed: 105 average time/residue: 0.1858 time to fit residues: 31.6417 Evaluate side-chains 101 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 51 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 107 optimal weight: 0.2980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.073551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056059 restraints weight = 57505.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057530 restraints weight = 27922.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058423 restraints weight = 17409.875| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12613 Z= 0.184 Angle : 0.631 11.612 17095 Z= 0.299 Chirality : 0.042 0.337 1958 Planarity : 0.003 0.042 2130 Dihedral : 5.437 85.925 1817 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.49 % Allowed : 15.40 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.22), residues: 1552 helix: 0.91 (0.21), residues: 604 sheet: -0.42 (0.32), residues: 276 loop : -1.11 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 35 HIS 0.002 0.001 HIS B 267 PHE 0.015 0.001 PHE A 578 TYR 0.009 0.001 TYR C 91 ARG 0.007 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.40 seconds wall clock time: 43 minutes 1.82 seconds (2581.82 seconds total)