Starting phenix.real_space_refine on Mon Jul 22 01:00:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr3_41569/07_2024/8tr3_41569.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr3_41569/07_2024/8tr3_41569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr3_41569/07_2024/8tr3_41569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr3_41569/07_2024/8tr3_41569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr3_41569/07_2024/8tr3_41569.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr3_41569/07_2024/8tr3_41569.cif" } resolution = 3.74 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= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 10305 2.51 5 N 2763 2.21 5 O 3234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "D ASP 589": "OD1" <-> "OD2" Residue "M PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ASP 474": "OD1" <-> "OD2" Residue "F ASP 589": "OD1" <-> "OD2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16401 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 16, 'TRANS': 295} Chain breaks: 5 Chain: "B" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 16, 'TRANS': 295} Chain breaks: 5 Chain: "D" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "M" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 16, 'TRANS': 295} Chain breaks: 5 Chain: "F" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.78, per 1000 atoms: 0.60 Number of scatterers: 16401 At special positions: 0 Unit cell: (147.396, 139.728, 99.684, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3234 8.00 N 2763 7.00 C 10305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " " NAG c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " " NAG p 1 " - " NAG p 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 230 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 363 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 413 " " NAG A 609 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 230 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 363 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 392 " " NAG C 608 " - " ASN C 413 " " NAG C 609 " - " ASN C 448 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 230 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 363 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 392 " " NAG E 608 " - " ASN E 413 " " NAG E 609 " - " ASN E 448 " " NAG P 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG c 1 " - " ASN C 241 " " NAG e 1 " - " ASN C 262 " " NAG p 1 " - " ASN E 241 " " NAG r 1 " - " ASN E 262 " Time building additional restraints: 6.42 Conformation dependent library (CDL) restraints added in 2.7 seconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3756 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 30 sheets defined 23.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.609A pdb=" N PHE A 391 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.696A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 removed outlier: 4.363A pdb=" N PHE B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.852A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 Processing helix chain 'B' and resid 562 through 596 removed outlier: 3.557A pdb=" N GLN B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 568 " --> pdb=" O HIS B 564 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.672A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 655 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.290A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.958A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.609A pdb=" N PHE C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.697A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 522 removed outlier: 4.363A pdb=" N PHE D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 removed outlier: 3.851A pdb=" N ILE D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 546 Processing helix chain 'D' and resid 562 through 596 removed outlier: 3.557A pdb=" N GLN D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR D 569 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.671A pdb=" N ILE D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 655 Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.291A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.958A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.609A pdb=" N PHE E 391 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.696A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 522 removed outlier: 4.363A pdb=" N PHE F 519 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU F 520 " --> pdb=" O GLY F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.852A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 546 Processing helix chain 'F' and resid 562 through 596 removed outlier: 3.557A pdb=" N GLN F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 568 " --> pdb=" O HIS F 564 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR F 569 " --> pdb=" O LEU F 565 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F 570 " --> pdb=" O LEU F 566 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.672A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 655 Processing helix chain 'J' and resid 28 through 31 Processing helix chain 'J' and resid 83 through 87 removed outlier: 4.290A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.959A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.504A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 244 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.509A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 334 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.686A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.102A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.504A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 244 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'C' and resid 260 through 261 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.509A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C 334 " --> pdb=" O ASN C 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 374 through 377 Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.686A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'M' and resid 10 through 14 removed outlier: 6.103A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS M 107 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA M 13 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA M 84 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.504A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 244 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC6, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.508A pdb=" N CYS E 445 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER E 334 " --> pdb=" O ASN E 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 374 through 377 Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.686A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.103A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA N 13 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5199 1.34 - 1.47: 4265 1.47 - 1.59: 7126 1.59 - 1.72: 3 1.72 - 1.85: 138 Bond restraints: 16731 Sorted by residual: bond pdb=" CD GLN I 6 " pdb=" NE2 GLN I 6 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.47e+01 bond pdb=" CD GLN H 6 " pdb=" NE2 GLN H 6 " ideal model delta sigma weight residual 1.328 1.248 0.080 2.10e-02 2.27e+03 1.45e+01 bond pdb=" CD GLN J 6 " pdb=" NE2 GLN J 6 " ideal model delta sigma weight residual 1.328 1.249 0.079 2.10e-02 2.27e+03 1.43e+01 bond pdb=" CD GLN J 1 " pdb=" NE2 GLN J 1 " ideal model delta sigma weight residual 1.328 1.250 0.078 2.10e-02 2.27e+03 1.38e+01 bond pdb=" CD GLN I 1 " pdb=" NE2 GLN I 1 " ideal model delta sigma weight residual 1.328 1.250 0.078 2.10e-02 2.27e+03 1.38e+01 ... (remaining 16726 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.48: 241 104.48 - 111.91: 8442 111.91 - 119.35: 5569 119.35 - 126.78: 8170 126.78 - 134.21: 300 Bond angle restraints: 22722 Sorted by residual: angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 106.43 5.57 1.40e+00 5.10e-01 1.58e+01 angle pdb=" CA PRO N 8 " pdb=" N PRO N 8 " pdb=" CD PRO N 8 " ideal model delta sigma weight residual 112.00 106.51 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA PRO M 8 " pdb=" N PRO M 8 " pdb=" CD PRO M 8 " ideal model delta sigma weight residual 112.00 106.52 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" CA GLN N 3 " pdb=" CB GLN N 3 " pdb=" CG GLN N 3 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA GLN L 3 " pdb=" CB GLN L 3 " pdb=" CG GLN L 3 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 ... (remaining 22717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 8902 16.75 - 33.51: 1198 33.51 - 50.26: 262 50.26 - 67.02: 81 67.02 - 83.77: 30 Dihedral angle restraints: 10473 sinusoidal: 4647 harmonic: 5826 Sorted by residual: dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -152.30 66.30 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual -86.00 -152.28 66.28 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -152.27 66.27 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 10470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2180 0.056 - 0.113: 441 0.113 - 0.169: 55 0.169 - 0.225: 3 0.225 - 0.282: 3 Chirality restraints: 2682 Sorted by residual: chirality pdb=" C1 NAG p 1 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG p 1 " pdb=" O5 NAG p 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2679 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 45 " 0.019 2.00e-02 2.50e+03 1.61e-02 6.50e+00 pdb=" CG TRP E 45 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 45 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 45 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 45 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 45 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 45 " 0.019 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP C 45 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 45 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 45 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 45 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 45 " 0.019 2.00e-02 2.50e+03 1.59e-02 6.34e+00 pdb=" CG TRP A 45 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 45 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 45 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 45 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 45 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 45 " 0.003 2.00e-02 2.50e+03 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3045 2.77 - 3.31: 15160 3.31 - 3.84: 26190 3.84 - 4.37: 28354 4.37 - 4.90: 50488 Nonbonded interactions: 123237 Sorted by model distance: nonbonded pdb=" O SER D 546 " pdb=" OG SER D 546 " model vdw 2.243 2.440 nonbonded pdb=" O SER B 546 " pdb=" OG SER B 546 " model vdw 2.243 2.440 nonbonded pdb=" O SER F 546 " pdb=" OG SER F 546 " model vdw 2.244 2.440 nonbonded pdb=" O ALA L 13 " pdb=" N LYS L 107 " model vdw 2.260 2.520 nonbonded pdb=" O ALA N 13 " pdb=" N LYS N 107 " model vdw 2.261 2.520 ... (remaining 123232 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'c' selection = chain 'e' selection = chain 'p' selection = chain 'r' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.620 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.005 0.111 16731 Z= 0.294 Angle : 0.720 9.756 22722 Z= 0.363 Chirality : 0.047 0.282 2682 Planarity : 0.004 0.041 2820 Dihedral : 16.049 83.772 6627 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.34 % Allowed : 25.47 % Favored : 74.19 % 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: -0.94 (0.20), residues: 1968 helix: 1.69 (0.28), residues: 396 sheet: -0.20 (0.20), residues: 678 loop : -2.09 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 45 HIS 0.004 0.001 HIS I 97 PHE 0.013 0.001 PHE J 29 TYR 0.008 0.001 TYR C 40 ARG 0.007 0.001 ARG D 644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 263 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 46 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7388 (mt-10) REVERT: N 105 GLU cc_start: 0.6753 (mp0) cc_final: 0.6395 (tm-30) outliers start: 6 outliers final: 3 residues processed: 263 average time/residue: 0.3321 time to fit residues: 122.7823 Evaluate side-chains 234 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain E residue 280 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.0770 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 229 ASN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 343 GLN A 404 GLN A 463 ASN B 577 GLN H 39 GLN H 97 HIS L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 229 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 343 GLN C 404 GLN C 463 ASN D 577 GLN I 39 GLN I 97 HIS M 38 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN E 229 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN E 343 GLN E 404 GLN E 463 ASN F 577 GLN J 39 GLN J 97 HIS N 38 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16731 Z= 0.256 Angle : 0.628 7.380 22722 Z= 0.323 Chirality : 0.045 0.192 2682 Planarity : 0.004 0.036 2820 Dihedral : 6.999 58.929 2973 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.72 % Allowed : 24.22 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1968 helix: 1.66 (0.27), residues: 396 sheet: -0.23 (0.20), residues: 678 loop : -2.24 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.004 0.001 HIS I 97 PHE 0.015 0.002 PHE E 376 TYR 0.018 0.001 TYR I 59 ARG 0.005 0.000 ARG I 82A *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 260 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7302 (mtt) cc_final: 0.6753 (mtt) REVERT: B 587 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8949 (mt) REVERT: H 66 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8290 (mtm-85) REVERT: H 80 MET cc_start: 0.7301 (tpt) cc_final: 0.7059 (tpt) REVERT: D 587 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8959 (mt) REVERT: I 46 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7452 (mt-10) REVERT: I 59 TYR cc_start: 0.7707 (m-10) cc_final: 0.7172 (m-10) REVERT: F 522 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7850 (t80) REVERT: J 46 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7591 (mt-10) outliers start: 48 outliers final: 29 residues processed: 287 average time/residue: 0.3237 time to fit residues: 133.5305 Evaluate side-chains 262 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 61 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16731 Z= 0.388 Angle : 0.699 7.635 22722 Z= 0.358 Chirality : 0.047 0.198 2682 Planarity : 0.004 0.036 2820 Dihedral : 7.028 59.360 2973 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 5.15 % Allowed : 24.00 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 1968 helix: 1.41 (0.27), residues: 402 sheet: -0.17 (0.20), residues: 648 loop : -2.36 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 610 HIS 0.006 0.001 HIS E 374 PHE 0.014 0.002 PHE E 376 TYR 0.019 0.002 TYR H 59 ARG 0.007 0.001 ARG J 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 256 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.7457 (m100) REVERT: B 530 MET cc_start: 0.7517 (mtt) cc_final: 0.7124 (mtt) REVERT: H 46 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7548 (mt-10) REVERT: H 66 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8226 (mtm-85) REVERT: C 479 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.6533 (m100) REVERT: D 587 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9024 (mm) REVERT: I 46 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7482 (mt-10) REVERT: E 479 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.6703 (m100) REVERT: F 522 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7935 (t80) REVERT: J 46 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7631 (mt-10) outliers start: 91 outliers final: 52 residues processed: 321 average time/residue: 0.3040 time to fit residues: 141.1928 Evaluate side-chains 295 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 238 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16731 Z= 0.377 Angle : 0.692 8.775 22722 Z= 0.355 Chirality : 0.047 0.254 2682 Planarity : 0.004 0.038 2820 Dihedral : 6.915 58.910 2973 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.98 % Allowed : 25.01 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 1968 helix: 1.34 (0.26), residues: 402 sheet: -0.20 (0.21), residues: 630 loop : -2.36 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 610 HIS 0.006 0.001 HIS E 374 PHE 0.014 0.002 PHE E 376 TYR 0.012 0.002 TYR C 486 ARG 0.009 0.001 ARG I 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 242 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7630 (m100) REVERT: B 530 MET cc_start: 0.7691 (mtt) cc_final: 0.7291 (mtt) REVERT: B 593 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8669 (tt) REVERT: H 46 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7472 (mt-10) REVERT: C 479 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.6681 (m100) REVERT: D 587 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9044 (mm) REVERT: I 46 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7519 (mt-10) REVERT: E 479 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.6803 (m100) REVERT: F 522 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7961 (t80) REVERT: J 46 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7597 (mt-10) REVERT: J 48 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7882 (mtm) REVERT: J 66 ARG cc_start: 0.8732 (mtm-85) cc_final: 0.8025 (ptm160) outliers start: 88 outliers final: 56 residues processed: 299 average time/residue: 0.2917 time to fit residues: 128.6914 Evaluate side-chains 292 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 229 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16731 Z= 0.205 Angle : 0.623 8.860 22722 Z= 0.317 Chirality : 0.045 0.244 2682 Planarity : 0.003 0.041 2820 Dihedral : 6.217 54.624 2973 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.87 % Allowed : 26.43 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1968 helix: 1.63 (0.27), residues: 402 sheet: -0.26 (0.21), residues: 657 loop : -2.32 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 338 HIS 0.002 0.001 HIS C 105 PHE 0.015 0.002 PHE C 376 TYR 0.014 0.001 TYR J 59 ARG 0.008 0.001 ARG J 82A *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 245 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: A 479 TRP cc_start: 0.8277 (OUTLIER) cc_final: 0.7441 (m100) REVERT: B 550 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.4545 (pp30) REVERT: B 593 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8580 (tt) REVERT: H 46 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7461 (mt-10) REVERT: H 48 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: L 62 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: L 105 GLU cc_start: 0.5287 (tm-30) cc_final: 0.4943 (tm-30) REVERT: C 103 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: C 104 MET cc_start: 0.8539 (ttm) cc_final: 0.7961 (ttm) REVERT: C 479 TRP cc_start: 0.8169 (OUTLIER) cc_final: 0.6590 (m100) REVERT: D 550 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.4505 (pp30) REVERT: D 587 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8990 (mt) REVERT: I 46 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7332 (mt-10) REVERT: I 66 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8060 (mtm-85) REVERT: E 103 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: E 479 TRP cc_start: 0.8201 (OUTLIER) cc_final: 0.6706 (m100) REVERT: F 522 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7993 (t80) REVERT: F 550 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.4586 (pp30) REVERT: J 46 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7442 (mt-10) REVERT: J 48 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7837 (mtm) REVERT: J 66 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8406 (mtm-85) REVERT: N 62 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8383 (m-80) outliers start: 86 outliers final: 45 residues processed: 309 average time/residue: 0.2955 time to fit residues: 135.7390 Evaluate side-chains 288 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 227 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain N residue 62 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 16731 Z= 0.593 Angle : 0.830 11.549 22722 Z= 0.422 Chirality : 0.051 0.225 2682 Planarity : 0.004 0.042 2820 Dihedral : 7.112 59.676 2973 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 6.56 % Allowed : 25.13 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1968 helix: 1.04 (0.26), residues: 402 sheet: -0.27 (0.21), residues: 627 loop : -2.57 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 338 HIS 0.007 0.002 HIS A 374 PHE 0.016 0.003 PHE M 98 TYR 0.018 0.002 TYR A 486 ARG 0.008 0.001 ARG J 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 234 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: A 384 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: A 479 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.7785 (m100) REVERT: B 530 MET cc_start: 0.7584 (mtt) cc_final: 0.7223 (mtt) REVERT: B 550 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.4441 (pp30) REVERT: B 593 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8673 (tt) REVERT: H 46 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7534 (mt-10) REVERT: H 48 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7881 (mtm) REVERT: H 66 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: L 62 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: L 103 LYS cc_start: 0.8085 (tptp) cc_final: 0.6981 (tptt) REVERT: L 105 GLU cc_start: 0.5534 (tm-30) cc_final: 0.5031 (mp0) REVERT: C 103 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: C 384 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: C 479 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.6807 (m100) REVERT: D 550 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.4352 (pp30) REVERT: D 587 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8937 (mm) REVERT: I 46 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7449 (mt-10) REVERT: I 48 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7851 (mmm) REVERT: E 103 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: E 384 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: E 479 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.6873 (m100) REVERT: F 522 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7905 (t80) REVERT: F 550 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.4462 (pp30) REVERT: J 46 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7580 (mt-10) REVERT: J 48 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7855 (mtm) outliers start: 116 outliers final: 76 residues processed: 320 average time/residue: 0.2734 time to fit residues: 131.5632 Evaluate side-chains 323 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 228 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 384 TYR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 384 TYR Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN C 229 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN N 79 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16731 Z= 0.226 Angle : 0.658 10.798 22722 Z= 0.333 Chirality : 0.045 0.219 2682 Planarity : 0.003 0.043 2820 Dihedral : 6.249 46.306 2973 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.64 % Allowed : 27.45 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1968 helix: 1.50 (0.27), residues: 402 sheet: -0.37 (0.21), residues: 663 loop : -2.44 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 112 HIS 0.003 0.001 HIS A 287 PHE 0.019 0.002 PHE E 376 TYR 0.009 0.001 TYR C 395 ARG 0.009 0.001 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 249 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: A 479 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.7444 (m100) REVERT: B 550 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.4400 (pp30) REVERT: B 593 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8590 (tt) REVERT: H 46 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7269 (mt-10) REVERT: H 66 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8245 (mtm-85) REVERT: L 62 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: L 103 LYS cc_start: 0.8170 (tptp) cc_final: 0.7089 (tptt) REVERT: C 103 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: C 104 MET cc_start: 0.8595 (ttm) cc_final: 0.7996 (ttm) REVERT: C 479 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.6768 (m100) REVERT: D 550 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.4436 (pp30) REVERT: I 46 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7308 (mt-10) REVERT: I 48 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7805 (mmm) REVERT: M 103 LYS cc_start: 0.7927 (tptp) cc_final: 0.7427 (ptmt) REVERT: M 105 GLU cc_start: 0.5598 (tm-30) cc_final: 0.4909 (mp0) REVERT: E 103 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: E 479 TRP cc_start: 0.8292 (OUTLIER) cc_final: 0.6849 (m100) REVERT: F 522 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.8091 (t80) REVERT: F 550 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.4570 (pp30) REVERT: J 46 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7403 (mt-10) REVERT: J 48 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7846 (mtm) REVERT: J 66 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8266 (mtm-85) REVERT: N 103 LYS cc_start: 0.7925 (tptp) cc_final: 0.7427 (ptmt) outliers start: 82 outliers final: 56 residues processed: 307 average time/residue: 0.2759 time to fit residues: 126.9621 Evaluate side-chains 302 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain N residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16731 Z= 0.214 Angle : 0.637 10.570 22722 Z= 0.321 Chirality : 0.044 0.224 2682 Planarity : 0.003 0.044 2820 Dihedral : 5.661 39.035 2973 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 4.58 % Allowed : 27.73 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1968 helix: 1.33 (0.27), residues: 420 sheet: -0.35 (0.21), residues: 663 loop : -2.40 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 112 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.002 PHE E 376 TYR 0.008 0.001 TYR C 395 ARG 0.009 0.000 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 244 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: A 479 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7304 (m100) REVERT: B 550 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.4608 (pp30) REVERT: B 593 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8530 (tt) REVERT: H 46 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7179 (mt-10) REVERT: L 62 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: L 105 GLU cc_start: 0.5957 (mp0) cc_final: 0.5588 (tm-30) REVERT: C 103 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: C 104 MET cc_start: 0.8554 (ttm) cc_final: 0.7926 (ttm) REVERT: C 479 TRP cc_start: 0.8207 (OUTLIER) cc_final: 0.6686 (m100) REVERT: D 550 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.4512 (pp30) REVERT: I 46 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6988 (mt-10) REVERT: I 48 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: I 66 ARG cc_start: 0.8734 (mtm-85) cc_final: 0.8501 (mtm-85) REVERT: M 103 LYS cc_start: 0.7957 (tptp) cc_final: 0.7444 (ptmt) REVERT: M 105 GLU cc_start: 0.5529 (tm-30) cc_final: 0.4981 (mp0) REVERT: E 103 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: E 479 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.6810 (m100) REVERT: F 522 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.8024 (t80) REVERT: F 550 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.4764 (pp30) REVERT: J 46 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7074 (mt-10) REVERT: N 105 GLU cc_start: 0.5607 (mp0) cc_final: 0.5264 (tm-30) outliers start: 81 outliers final: 56 residues processed: 304 average time/residue: 0.2955 time to fit residues: 134.3298 Evaluate side-chains 297 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 228 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 160 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16731 Z= 0.263 Angle : 0.667 13.739 22722 Z= 0.336 Chirality : 0.045 0.205 2682 Planarity : 0.004 0.041 2820 Dihedral : 5.593 39.962 2973 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 4.81 % Allowed : 28.07 % Favored : 67.12 % 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: -1.32 (0.20), residues: 1968 helix: 1.29 (0.27), residues: 420 sheet: -0.34 (0.20), residues: 663 loop : -2.45 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 112 HIS 0.004 0.001 HIS A 287 PHE 0.017 0.002 PHE M 62 TYR 0.008 0.001 TYR J 91 ARG 0.014 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 234 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: A 479 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7291 (m100) REVERT: B 550 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.4640 (pp30) REVERT: B 593 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8558 (tt) REVERT: H 46 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7133 (mt-10) REVERT: L 18 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7957 (ttp80) REVERT: L 62 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: L 105 GLU cc_start: 0.5977 (mp0) cc_final: 0.5508 (tm-30) REVERT: C 103 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: C 479 TRP cc_start: 0.8250 (OUTLIER) cc_final: 0.6724 (m100) REVERT: D 550 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.4527 (pp30) REVERT: I 46 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6950 (mt-10) REVERT: I 48 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7840 (mmm) REVERT: I 66 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8477 (mtm-85) REVERT: E 103 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8751 (tt0) REVERT: E 479 TRP cc_start: 0.8249 (OUTLIER) cc_final: 0.6787 (m100) REVERT: F 522 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7989 (t80) REVERT: F 550 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.4747 (pp30) REVERT: J 46 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7006 (mt-10) REVERT: N 105 GLU cc_start: 0.5975 (mp0) cc_final: 0.5755 (tm-30) outliers start: 85 outliers final: 63 residues processed: 298 average time/residue: 0.2771 time to fit residues: 123.7395 Evaluate side-chains 299 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 223 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16731 Z= 0.352 Angle : 0.719 14.680 22722 Z= 0.363 Chirality : 0.046 0.232 2682 Planarity : 0.004 0.041 2820 Dihedral : 5.868 46.759 2973 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 4.70 % Allowed : 28.52 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1968 helix: 1.42 (0.27), residues: 402 sheet: -0.39 (0.21), residues: 654 loop : -2.58 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 112 HIS 0.005 0.001 HIS A 287 PHE 0.017 0.002 PHE M 62 TYR 0.010 0.001 TYR C 486 ARG 0.007 0.001 ARG J 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 225 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: A 479 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.7496 (m100) REVERT: B 550 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.4640 (pp30) REVERT: B 593 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8612 (tt) REVERT: L 18 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7927 (ttp80) REVERT: L 62 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: L 105 GLU cc_start: 0.6072 (mp0) cc_final: 0.5689 (tm-30) REVERT: C 103 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: C 479 TRP cc_start: 0.8373 (OUTLIER) cc_final: 0.6757 (m100) REVERT: D 550 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.4497 (pp30) REVERT: I 46 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6947 (mt-10) REVERT: I 48 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7575 (mtm) REVERT: I 66 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8494 (mtm-85) REVERT: E 103 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: E 479 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.6883 (m100) REVERT: F 522 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7953 (t80) REVERT: F 550 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.4662 (pp30) REVERT: N 105 GLU cc_start: 0.5616 (mp0) cc_final: 0.5031 (tm-30) outliers start: 83 outliers final: 62 residues processed: 288 average time/residue: 0.2811 time to fit residues: 121.8455 Evaluate side-chains 294 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 219 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 287 HIS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 598 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN E 229 ASN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.088927 restraints weight = 37397.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089186 restraints weight = 24892.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089926 restraints weight = 20971.535| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16731 Z= 0.227 Angle : 0.667 14.339 22722 Z= 0.336 Chirality : 0.045 0.207 2682 Planarity : 0.004 0.044 2820 Dihedral : 5.443 38.280 2973 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.19 % Allowed : 28.92 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1968 helix: 1.27 (0.26), residues: 420 sheet: -0.32 (0.20), residues: 654 loop : -2.48 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 103 HIS 0.003 0.001 HIS C 374 PHE 0.017 0.002 PHE M 62 TYR 0.008 0.001 TYR I 91 ARG 0.007 0.001 ARG J 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3440.45 seconds wall clock time: 62 minutes 55.27 seconds (3775.27 seconds total)