Starting phenix.real_space_refine on Sat Mar 16 09:58:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpx_36489/03_2024/8jpx_36489.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpx_36489/03_2024/8jpx_36489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpx_36489/03_2024/8jpx_36489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpx_36489/03_2024/8jpx_36489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpx_36489/03_2024/8jpx_36489.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpx_36489/03_2024/8jpx_36489.pdb" } resolution = 2.9 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= 0.007 sd= 0.116 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: 6 Type Number sf(0) Gaussians P 78 5.49 5 Mg 6 5.21 5 S 38 5.16 5 C 9042 2.51 5 N 2386 2.21 5 O 2812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A TYR 768": "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: 14362 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 6380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6380 Classifications: {'peptide': 770} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 740} Chain: "H" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 342 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 336 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 6380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6380 Classifications: {'peptide': 770} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 740} Chain: "G" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 342 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "T" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 336 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.21, per 1000 atoms: 0.57 Number of scatterers: 14362 At special positions: 0 Unit cell: (111.35, 106.25, 109.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 78 15.00 Mg 6 11.99 O 2812 8.00 N 2386 7.00 C 9042 6.00 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 - 3.50 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 Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 2.5 seconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 18 sheets defined 36.2% alpha, 24.3% beta 28 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.08 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.524A pdb=" N ILE B 16 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.552A pdb=" N LEU B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.685A pdb=" N LYS B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 removed outlier: 3.629A pdb=" N LYS B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.806A pdb=" N TYR B 221 " --> pdb=" O HIS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 236 removed outlier: 3.945A pdb=" N GLU B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.853A pdb=" N GLU B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.514A pdb=" N LEU B 347 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 393 through 411 removed outlier: 3.583A pdb=" N MET B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 421 removed outlier: 3.829A pdb=" N LEU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 467 Processing helix chain 'B' and resid 487 through 498 removed outlier: 3.718A pdb=" N LEU B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 523 through 538 Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.768A pdb=" N ASP B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 647 removed outlier: 3.523A pdb=" N LYS B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 645 " --> pdb=" O TYR B 641 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 647 " --> pdb=" O SER B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 removed outlier: 3.511A pdb=" N VAL B 717 " --> pdb=" O THR B 713 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 725 " --> pdb=" O PHE B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 753 removed outlier: 3.511A pdb=" N LYS B 746 " --> pdb=" O HIS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.619A pdb=" N GLY B 765 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.555A pdb=" N ILE A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.538A pdb=" N LEU A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.682A pdb=" N LYS A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.629A pdb=" N LYS A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 Processing helix chain 'A' and resid 206 through 222 removed outlier: 3.813A pdb=" N TYR A 221 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.948A pdb=" N GLU A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.852A pdb=" N GLU A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.502A pdb=" N LEU A 347 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 393 through 411 removed outlier: 3.563A pdb=" N MET A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.832A pdb=" N LEU A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 487 through 498 removed outlier: 3.711A pdb=" N LEU A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 523 through 538 Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.772A pdb=" N ASP A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 647 removed outlier: 3.524A pdb=" N LYS A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 645 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.580A pdb=" N VAL A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 725 " --> pdb=" O PHE A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 removed outlier: 3.512A pdb=" N LYS A 746 " --> pdb=" O HIS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.702A pdb=" N GLY A 765 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.663A pdb=" N SER B 317 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU B 320 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN B 672 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 696 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE B 656 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS B 698 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP B 654 " --> pdb=" O LYS B 698 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 553 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP B 628 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 559 " --> pdb=" O ASP B 628 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 570 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY B 591 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 572 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS B 589 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 574 " --> pdb=" O PRO B 587 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE B 576 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 585 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.663A pdb=" N SER B 317 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU B 320 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN B 672 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.387A pdb=" N ILE B 59 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE B 21 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU B 77 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 23 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195 removed outlier: 4.851A pdb=" N LYS B 200 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.747A pdb=" N VAL B 544 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 448 removed outlier: 3.500A pdb=" N GLU B 448 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 473 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLN B 503 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 475 " --> pdb=" O GLN B 503 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 505 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 477 " --> pdb=" O VAL B 505 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.664A pdb=" N SER A 317 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU A 320 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 672 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU A 696 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A 656 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS A 698 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 654 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 553 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 628 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 559 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 570 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY A 591 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 572 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYS A 589 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 574 " --> pdb=" O PRO A 587 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 576 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 585 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.664A pdb=" N SER A 317 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU A 320 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 672 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AB4, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.386A pdb=" N ILE A 59 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 21 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU A 77 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 23 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AB6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AB7, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.865A pdb=" N LYS A 200 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 332 through 333 removed outlier: 3.724A pdb=" N VAL A 544 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.560A pdb=" N GLY A 473 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLN A 503 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 475 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL A 505 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 477 " --> pdb=" O VAL A 505 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3610 1.33 - 1.45: 2848 1.45 - 1.57: 8108 1.57 - 1.69: 152 1.69 - 1.81: 74 Bond restraints: 14792 Sorted by residual: bond pdb=" CB PRO B 185 " pdb=" CG PRO B 185 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 bond pdb=" C LEU B 263 " pdb=" N LEU B 264 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.67e-02 3.59e+03 1.83e+00 bond pdb=" CB ASP B 310 " pdb=" CG ASP B 310 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" O4' DG H 15 " pdb=" C1' DG H 15 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.01e-01 bond pdb=" C4' DG G 12 " pdb=" O4' DG G 12 " ideal model delta sigma weight residual 1.450 1.431 0.019 2.00e-02 2.50e+03 8.98e-01 ... (remaining 14787 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.85: 611 105.85 - 112.92: 7901 112.92 - 119.98: 5244 119.98 - 127.05: 6247 127.05 - 134.12: 243 Bond angle restraints: 20246 Sorted by residual: angle pdb=" N LEU A 158 " pdb=" CA LEU A 158 " pdb=" C LEU A 158 " ideal model delta sigma weight residual 114.62 109.88 4.74 1.14e+00 7.69e-01 1.73e+01 angle pdb=" N LEU B 158 " pdb=" CA LEU B 158 " pdb=" C LEU B 158 " ideal model delta sigma weight residual 114.62 109.94 4.68 1.14e+00 7.69e-01 1.69e+01 angle pdb=" CA LEU A 158 " pdb=" C LEU A 158 " pdb=" N VAL A 159 " ideal model delta sigma weight residual 119.71 116.28 3.43 1.17e+00 7.31e-01 8.62e+00 angle pdb=" CA LEU B 158 " pdb=" C LEU B 158 " pdb=" N VAL B 159 " ideal model delta sigma weight residual 119.71 116.35 3.36 1.17e+00 7.31e-01 8.27e+00 angle pdb=" C ASP B 577 " pdb=" N SER B 578 " pdb=" CA SER B 578 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 ... (remaining 20241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.45: 8043 31.45 - 62.90: 780 62.90 - 94.34: 43 94.34 - 125.79: 0 125.79 - 157.24: 4 Dihedral angle restraints: 8870 sinusoidal: 4294 harmonic: 4576 Sorted by residual: dihedral pdb=" C4' DT F 2 " pdb=" C3' DT F 2 " pdb=" O3' DT F 2 " pdb=" P DT F 3 " ideal model delta sinusoidal sigma weight residual 220.00 62.76 157.24 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DT E 2 " pdb=" C3' DT E 2 " pdb=" O3' DT E 2 " pdb=" P DT E 3 " ideal model delta sinusoidal sigma weight residual 220.00 76.92 143.08 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" CA ASP B 438 " pdb=" C ASP B 438 " pdb=" N PHE B 439 " pdb=" CA PHE B 439 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1468 0.034 - 0.067: 503 0.067 - 0.101: 153 0.101 - 0.134: 104 0.134 - 0.168: 6 Chirality restraints: 2234 Sorted by residual: chirality pdb=" CB ILE B 616 " pdb=" CA ILE B 616 " pdb=" CG1 ILE B 616 " pdb=" CG2 ILE B 616 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE A 616 " pdb=" CA ILE A 616 " pdb=" CG1 ILE A 616 " pdb=" CG2 ILE A 616 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE B 694 " pdb=" N ILE B 694 " pdb=" C ILE B 694 " pdb=" CB ILE B 694 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2231 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 583 " 0.237 9.50e-02 1.11e+02 1.06e-01 7.02e+00 pdb=" NE ARG B 583 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 583 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 583 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 583 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 162 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO B 163 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 29 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO B 30 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.028 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 56 2.50 - 3.10: 9340 3.10 - 3.70: 20429 3.70 - 4.30: 31713 4.30 - 4.90: 53439 Nonbonded interactions: 114977 Sorted by model distance: nonbonded pdb=" OP1 DT U 10 " pdb="MG MG B 801 " model vdw 1.900 2.170 nonbonded pdb=" OP1 DT T 10 " pdb="MG MG A 801 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP A 558 " pdb="MG MG A 801 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP B 558 " pdb="MG MG B 801 " model vdw 1.903 2.170 nonbonded pdb=" ND1 HIS A 745 " pdb="MG MG A 801 " model vdw 2.008 2.250 ... (remaining 114972 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' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'T' selection = chain 'U' } 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 individual isotropic 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: 0.370 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: 2.680 Check model and map are aligned: 0.210 Set scattering table: 0.160 Process input model: 45.660 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.003 0.074 14792 Z= 0.197 Angle : 0.562 10.203 20246 Z= 0.322 Chirality : 0.043 0.168 2234 Planarity : 0.005 0.106 2296 Dihedral : 21.049 157.240 5914 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.50 % Allowed : 34.07 % Favored : 65.44 % 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: -0.57 (0.22), residues: 1536 helix: 0.50 (0.25), residues: 496 sheet: 1.00 (0.28), residues: 342 loop : -1.80 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.002 0.001 HIS B 144 PHE 0.032 0.001 PHE A 439 TYR 0.013 0.001 TYR A 212 ARG 0.007 0.000 ARG B 521 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 173 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 287 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 443 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6326 (mt-10) REVERT: A 31 GLU cc_start: 0.7551 (tp30) cc_final: 0.7227 (tp30) REVERT: A 36 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7360 (mttm) REVERT: A 443 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6259 (mt-10) outliers start: 7 outliers final: 6 residues processed: 174 average time/residue: 1.5788 time to fit residues: 297.0520 Evaluate side-chains 166 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 596 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.0870 chunk 123 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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: 0.8658 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14792 Z= 0.269 Angle : 0.561 8.904 20246 Z= 0.314 Chirality : 0.044 0.140 2234 Planarity : 0.005 0.051 2296 Dihedral : 18.241 168.216 2540 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.83 % Allowed : 34.70 % Favored : 62.46 % 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: -0.42 (0.22), residues: 1536 helix: 0.83 (0.25), residues: 492 sheet: 0.68 (0.27), residues: 366 loop : -1.70 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 222 HIS 0.003 0.001 HIS B 144 PHE 0.031 0.001 PHE A 439 TYR 0.013 0.001 TYR A 743 ARG 0.006 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6302 (mt-10) REVERT: B 592 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: B 611 PHE cc_start: 0.6339 (m-10) cc_final: 0.5886 (m-80) REVERT: A 31 GLU cc_start: 0.7689 (tp30) cc_final: 0.7339 (tp30) REVERT: A 36 LYS cc_start: 0.7612 (ttmt) cc_final: 0.7340 (mttm) REVERT: A 443 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6288 (mt-10) REVERT: A 592 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7996 (pt0) outliers start: 40 outliers final: 22 residues processed: 189 average time/residue: 1.4697 time to fit residues: 301.9387 Evaluate side-chains 180 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 709 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 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: 0.8668 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14792 Z= 0.292 Angle : 0.570 8.304 20246 Z= 0.318 Chirality : 0.045 0.142 2234 Planarity : 0.005 0.053 2296 Dihedral : 18.014 155.151 2532 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.12 % Rotamer: Outliers : 3.97 % Allowed : 34.92 % Favored : 61.12 % 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: -0.40 (0.22), residues: 1536 helix: 0.89 (0.24), residues: 492 sheet: 0.64 (0.27), residues: 378 loop : -1.73 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 222 HIS 0.003 0.001 HIS B 144 PHE 0.032 0.002 PHE A 439 TYR 0.014 0.001 TYR B 743 ARG 0.006 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 162 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8554 (tt) REVERT: B 443 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6358 (mt-10) REVERT: B 592 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: A 31 GLU cc_start: 0.7820 (tp30) cc_final: 0.7611 (tp30) REVERT: A 36 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7265 (mttm) REVERT: A 443 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6302 (mt-10) REVERT: A 592 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: A 622 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8533 (mtmt) outliers start: 56 outliers final: 32 residues processed: 198 average time/residue: 1.3580 time to fit residues: 293.1171 Evaluate side-chains 191 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 716 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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: 0.8673 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14792 Z= 0.301 Angle : 0.573 7.885 20246 Z= 0.320 Chirality : 0.045 0.144 2234 Planarity : 0.004 0.051 2296 Dihedral : 18.065 155.448 2532 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.01 % Favored : 91.86 % Rotamer: Outliers : 4.67 % Allowed : 34.84 % Favored : 60.48 % 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: 1536 helix: 0.73 (0.24), residues: 504 sheet: 0.78 (0.27), residues: 364 loop : -1.75 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 222 HIS 0.003 0.001 HIS B 144 PHE 0.032 0.002 PHE A 439 TYR 0.014 0.001 TYR B 743 ARG 0.005 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 169 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 252 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.5752 (mtmm) REVERT: B 443 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6339 (mt-10) REVERT: B 622 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8647 (mtmt) REVERT: A 36 LYS cc_start: 0.7609 (ttmt) cc_final: 0.7266 (mttm) REVERT: A 252 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.5742 (mtmm) REVERT: A 380 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7414 (mtt180) REVERT: A 443 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6349 (mt-10) REVERT: A 458 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: A 622 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8521 (mtmt) outliers start: 66 outliers final: 40 residues processed: 216 average time/residue: 1.4774 time to fit residues: 346.1882 Evaluate side-chains 205 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 159 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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: 0.8683 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14792 Z= 0.330 Angle : 0.590 7.797 20246 Z= 0.329 Chirality : 0.046 0.144 2234 Planarity : 0.004 0.051 2296 Dihedral : 18.101 164.556 2530 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 4.96 % Allowed : 34.77 % Favored : 60.27 % 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: -0.47 (0.22), residues: 1536 helix: 0.76 (0.24), residues: 498 sheet: 0.99 (0.28), residues: 350 loop : -1.89 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 222 HIS 0.003 0.001 HIS A 742 PHE 0.032 0.002 PHE A 439 TYR 0.015 0.001 TYR B 743 ARG 0.006 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 166 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7551 (t80) REVERT: B 66 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8598 (tt) REVERT: B 252 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.5770 (mtmm) REVERT: B 380 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7385 (mtt180) REVERT: B 443 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6338 (mt-10) REVERT: B 622 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8618 (mtmt) REVERT: B 758 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8033 (tppp) REVERT: A 36 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7249 (mttm) REVERT: A 252 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.5752 (mtmm) REVERT: A 443 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6377 (mt-10) REVERT: A 458 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7777 (mt-10) outliers start: 70 outliers final: 43 residues processed: 219 average time/residue: 1.4521 time to fit residues: 344.9710 Evaluate side-chains 201 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 150 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 758 LYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.8718 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 14792 Z= 0.517 Angle : 0.678 8.476 20246 Z= 0.374 Chirality : 0.050 0.154 2234 Planarity : 0.005 0.051 2296 Dihedral : 18.285 161.930 2530 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.05 % Favored : 90.82 % Rotamer: Outliers : 6.02 % Allowed : 34.14 % Favored : 59.84 % 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: -0.68 (0.22), residues: 1536 helix: 0.62 (0.24), residues: 488 sheet: 0.77 (0.27), residues: 360 loop : -1.98 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 222 HIS 0.004 0.001 HIS B 742 PHE 0.040 0.002 PHE B 439 TYR 0.021 0.002 TYR B 743 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 150 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7597 (t80) REVERT: B 66 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8700 (tt) REVERT: B 252 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.5859 (mtmm) REVERT: B 380 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7342 (mtt180) REVERT: B 458 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: A 36 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7223 (mttm) REVERT: A 252 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.5828 (mtmm) REVERT: A 443 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6434 (mt-10) REVERT: A 458 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: A 592 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8167 (pt0) outliers start: 85 outliers final: 48 residues processed: 217 average time/residue: 1.4212 time to fit residues: 335.3064 Evaluate side-chains 201 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 145 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14792 Z= 0.231 Angle : 0.562 7.332 20246 Z= 0.316 Chirality : 0.044 0.142 2234 Planarity : 0.004 0.051 2296 Dihedral : 18.126 162.918 2530 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.36 % Favored : 92.51 % Rotamer: Outliers : 4.18 % Allowed : 35.62 % Favored : 60.20 % 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: -0.48 (0.22), residues: 1536 helix: 0.74 (0.24), residues: 504 sheet: 0.74 (0.27), residues: 358 loop : -1.78 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 222 HIS 0.003 0.001 HIS B 144 PHE 0.033 0.001 PHE A 439 TYR 0.013 0.001 TYR A 212 ARG 0.005 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 159 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 66 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8571 (tt) REVERT: B 232 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: B 252 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7024 (mptt) REVERT: B 443 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6333 (mt-10) REVERT: B 458 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: B 622 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8581 (mtmt) REVERT: A 36 LYS cc_start: 0.7635 (ttmt) cc_final: 0.7228 (mttm) REVERT: A 252 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6947 (mptt) REVERT: A 443 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6253 (mt-10) REVERT: A 458 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: A 592 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7939 (pt0) outliers start: 59 outliers final: 35 residues processed: 203 average time/residue: 1.4418 time to fit residues: 318.4929 Evaluate side-chains 197 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 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 672 ASN A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14792 Z= 0.319 Angle : 0.597 7.757 20246 Z= 0.334 Chirality : 0.046 0.144 2234 Planarity : 0.005 0.050 2296 Dihedral : 18.187 160.905 2530 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.14 % Favored : 91.73 % Rotamer: Outliers : 4.46 % Allowed : 35.91 % Favored : 59.63 % 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: -0.47 (0.22), residues: 1536 helix: 0.86 (0.24), residues: 492 sheet: 0.99 (0.28), residues: 340 loop : -1.92 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 222 HIS 0.003 0.001 HIS A 742 PHE 0.032 0.002 PHE A 439 TYR 0.014 0.001 TYR B 743 ARG 0.005 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 156 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 66 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8615 (tt) REVERT: B 458 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: B 622 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8526 (mtmt) REVERT: A 36 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7213 (mttm) REVERT: A 252 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.5797 (mtmm) REVERT: A 380 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7386 (mtt180) REVERT: A 443 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6370 (mt-10) REVERT: A 458 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7815 (mt-10) outliers start: 63 outliers final: 43 residues processed: 205 average time/residue: 1.3893 time to fit residues: 309.9011 Evaluate side-chains 199 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 111 optimal weight: 0.4980 chunk 43 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14792 Z= 0.275 Angle : 0.586 7.517 20246 Z= 0.328 Chirality : 0.045 0.143 2234 Planarity : 0.004 0.051 2296 Dihedral : 18.184 160.959 2530 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.36 % Favored : 92.51 % Rotamer: Outliers : 3.61 % Allowed : 36.90 % Favored : 59.49 % 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: -0.42 (0.22), residues: 1536 helix: 0.91 (0.24), residues: 492 sheet: 1.01 (0.28), residues: 340 loop : -1.89 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 222 HIS 0.003 0.001 HIS B 742 PHE 0.032 0.002 PHE A 439 TYR 0.013 0.001 TYR A 360 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 151 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7526 (t80) REVERT: B 66 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 443 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6380 (mt-10) REVERT: B 458 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: B 471 GLU cc_start: 0.8286 (pm20) cc_final: 0.8085 (pm20) REVERT: B 622 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8550 (mtmt) REVERT: A 36 LYS cc_start: 0.7662 (ttmt) cc_final: 0.7256 (mttm) REVERT: A 252 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7171 (mptt) REVERT: A 380 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7392 (mtt180) REVERT: A 443 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6269 (mt-10) REVERT: A 458 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7814 (mt-10) outliers start: 51 outliers final: 43 residues processed: 190 average time/residue: 1.4296 time to fit residues: 295.0728 Evaluate side-chains 198 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 148 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14792 Z= 0.414 Angle : 0.651 8.341 20246 Z= 0.361 Chirality : 0.048 0.149 2234 Planarity : 0.005 0.050 2296 Dihedral : 18.317 161.046 2530 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.40 % Favored : 91.47 % Rotamer: Outliers : 3.97 % Allowed : 36.61 % Favored : 59.42 % 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: -0.63 (0.22), residues: 1536 helix: 0.60 (0.24), residues: 500 sheet: 0.93 (0.28), residues: 336 loop : -1.93 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 222 HIS 0.003 0.001 HIS A 742 PHE 0.034 0.002 PHE B 439 TYR 0.017 0.002 TYR A 743 ARG 0.004 0.000 ARG A 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 146 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7527 (t80) REVERT: B 66 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8672 (tt) REVERT: B 458 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: B 622 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8520 (mtmt) REVERT: A 36 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7240 (mttm) REVERT: A 380 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7363 (mtt180) REVERT: A 443 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6460 (mt-10) REVERT: A 458 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: A 592 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8104 (pt0) outliers start: 56 outliers final: 43 residues processed: 191 average time/residue: 1.5355 time to fit residues: 318.7251 Evaluate side-chains 194 residues out of total 1412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.128897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098164 restraints weight = 19427.085| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.21 r_work: 0.2967 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14792 Z= 0.203 Angle : 0.561 6.722 20246 Z= 0.316 Chirality : 0.044 0.144 2234 Planarity : 0.004 0.053 2296 Dihedral : 18.135 160.988 2530 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.23 % Favored : 92.64 % Rotamer: Outliers : 3.12 % Allowed : 37.54 % Favored : 59.35 % 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: -0.39 (0.22), residues: 1536 helix: 0.82 (0.24), residues: 510 sheet: 0.78 (0.27), residues: 358 loop : -1.74 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 222 HIS 0.002 0.001 HIS B 144 PHE 0.032 0.001 PHE A 439 TYR 0.015 0.001 TYR B 212 ARG 0.003 0.000 ARG A 583 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5303.33 seconds wall clock time: 94 minutes 20.15 seconds (5660.15 seconds total)