Starting phenix.real_space_refine on Wed Apr 10 16:21:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saz_40285/04_2024/8saz_40285_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saz_40285/04_2024/8saz_40285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saz_40285/04_2024/8saz_40285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saz_40285/04_2024/8saz_40285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saz_40285/04_2024/8saz_40285_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saz_40285/04_2024/8saz_40285_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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 132 5.16 5 C 12453 2.51 5 N 3327 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 230": "OD1" <-> "OD2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 172": "OE1" <-> "OE2" Residue "K TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 370": "OE1" <-> "OE2" Residue "K PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19960 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "F" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.61, per 1000 atoms: 0.53 Number of scatterers: 19960 At special positions: 0 Unit cell: (158.36, 161.57, 139.1, 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 132 16.00 O 4048 8.00 N 3327 7.00 C 12453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 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=2.03 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 C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 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=2.03 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.02 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.04 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 10 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 10 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " " BMA J 3 " - " MAN J 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG G 1 " - " ASN E 332 " " NAG J 1 " - " ASN E 301 " " NAG O 1 " - " ASN E 156 " " NAG P 1 " - " ASN E 442 " " NAG Q 1 " - " ASN K 301 " " NAG R 1 " - " ASN K 156 " " NAG S 1 " - " ASN K 332 " " NAG T 1 " - " ASN K 442 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 156 " " NAG X 1 " - " ASN A 442 " Time building additional restraints: 8.79 Conformation dependent library (CDL) restraints added in 3.5 seconds 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 33 sheets defined 20.6% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.786A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 62 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.370A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.693A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.879A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 594 removed outlier: 4.096A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.994A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 654 removed outlier: 3.720A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 4.004A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.710A pdb=" N ALA E 60 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.364A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.508A pdb=" N GLU E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.016A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 594 removed outlier: 4.085A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 597 No H-bonds generated for 'chain 'F' and resid 595 through 597' Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.043A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 654 removed outlier: 3.714A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 660 removed outlier: 3.908A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.809A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU K 62 " --> pdb=" O ARG K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.438A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 3.665A pdb=" N CYS K 126 " --> pdb=" O THR K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 350 Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 474 through 481 removed outlier: 4.186A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 535 removed outlier: 4.164A pdb=" N MET L 535 " --> pdb=" O GLY L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 542 removed outlier: 4.083A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 4.058A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP L 589 " --> pdb=" O ARG L 585 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE L 595 " --> pdb=" O GLN L 591 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 635 removed outlier: 4.073A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 660 removed outlier: 3.732A pdb=" N ILE L 642 " --> pdb=" O TYR L 638 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN L 650 " --> pdb=" O LEU L 646 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS L 655 " --> pdb=" O ASN L 651 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU L 657 " --> pdb=" O GLN L 653 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN L 658 " --> pdb=" O GLU L 654 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.531A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 4.699A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.215A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.700A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 382 through 386 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.757A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.602A pdb=" N THR C 121 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.848A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.468A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.324A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.787A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AB7, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.242A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.717A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 386 current: chain 'E' and resid 467 through 470 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 11 current: chain 'H' and resid 45 through 51 removed outlier: 3.602A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 116 through 117 Processing sheet with id=AC2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.555A pdb=" N VAL I 10 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 23 Processing sheet with id=AC4, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.264A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL L 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL K 38 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR L 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR K 40 " --> pdb=" O CYS L 604 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N CYS L 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 45 through 46 removed outlier: 4.058A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 91 through 94 removed outlier: 4.798A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 169 through 176 Processing sheet with id=AC9, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.244A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 261 current: chain 'K' and resid 284 through 308 removed outlier: 6.700A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 316 through 323 current: chain 'K' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 382 through 386 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD2, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.739A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.502A pdb=" N THR M 121 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.535A pdb=" N VAL N 10 " --> pdb=" O LYS N 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 20 through 23 removed outlier: 3.559A pdb=" N SER N 67 " --> pdb=" O SER N 74 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 46 through 51 removed outlier: 6.510A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR N 51 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL N 35 " --> pdb=" O TYR N 51 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1353 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: 6.34 Time building geometry restraints manager: 9.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6311 1.35 - 1.48: 5347 1.48 - 1.61: 8536 1.61 - 1.73: 3 1.73 - 1.86: 177 Bond restraints: 20374 Sorted by residual: bond pdb=" C1 MAN G 8 " pdb=" C2 MAN G 8 " ideal model delta sigma weight residual 1.526 1.613 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 MAN S 8 " pdb=" C2 MAN S 8 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 MAN V 8 " pdb=" C2 MAN V 8 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CG PRO I 57 " pdb=" CD PRO I 57 " ideal model delta sigma weight residual 1.503 1.366 0.137 3.40e-02 8.65e+02 1.63e+01 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.483 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 20369 not shown) Histogram of bond angle deviations from ideal: 84.09 - 94.29: 4 94.29 - 104.48: 289 104.48 - 114.68: 12530 114.68 - 124.87: 14376 124.87 - 135.07: 500 Bond angle restraints: 27699 Sorted by residual: angle pdb=" N PRO I 57 " pdb=" CD PRO I 57 " pdb=" CG PRO I 57 " ideal model delta sigma weight residual 103.20 84.09 19.11 1.50e+00 4.44e-01 1.62e+02 angle pdb=" CA PRO I 57 " pdb=" CB PRO I 57 " pdb=" CG PRO I 57 " ideal model delta sigma weight residual 104.50 88.15 16.35 1.90e+00 2.77e-01 7.40e+01 angle pdb=" N PRO D 57 " pdb=" CD PRO D 57 " pdb=" CG PRO D 57 " ideal model delta sigma weight residual 103.20 90.68 12.52 1.50e+00 4.44e-01 6.96e+01 angle pdb=" CA PRO D 57 " pdb=" CB PRO D 57 " pdb=" CG PRO D 57 " ideal model delta sigma weight residual 104.50 92.14 12.36 1.90e+00 2.77e-01 4.23e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 131.15 -9.45 1.80e+00 3.09e-01 2.75e+01 ... (remaining 27694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.44: 12104 22.44 - 44.88: 678 44.88 - 67.32: 103 67.32 - 89.76: 96 89.76 - 112.20: 47 Dihedral angle restraints: 13028 sinusoidal: 5924 harmonic: 7104 Sorted by residual: dihedral pdb=" CA CYS K 196 " pdb=" C CYS K 196 " pdb=" N ASN K 197 " pdb=" CA ASN K 197 " ideal model delta harmonic sigma weight residual 180.00 145.55 34.45 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" CA VAL B 570 " pdb=" C VAL B 570 " pdb=" N TRP B 571 " pdb=" CA TRP B 571 " ideal model delta harmonic sigma weight residual 180.00 147.95 32.05 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -31.13 -54.87 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 13025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2700 0.062 - 0.124: 473 0.124 - 0.186: 112 0.186 - 0.248: 3 0.248 - 0.311: 13 Chirality restraints: 3301 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 156 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 156 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3298 not shown) Planarity restraints: 3453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 56 " -0.581 9.50e-02 1.11e+02 2.60e-01 4.16e+01 pdb=" NE ARG N 56 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG N 56 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG N 56 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG N 56 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 116 " 0.016 2.00e-02 2.50e+03 1.83e-02 6.71e+00 pdb=" CG TYR M 116 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR M 116 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR M 116 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 116 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR M 116 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR M 116 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR M 116 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 106 " -0.022 2.00e-02 2.50e+03 1.48e-02 4.39e+00 pdb=" CG TYR C 106 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 106 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 106 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 106 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 106 " -0.006 2.00e-02 2.50e+03 ... (remaining 3450 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 837 2.71 - 3.26: 19898 3.26 - 3.81: 29852 3.81 - 4.35: 38089 4.35 - 4.90: 65567 Nonbonded interactions: 154243 Sorted by model distance: nonbonded pdb=" OG1 THR K 163 " pdb=" OE1 GLU K 164 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR A 163 " pdb=" OE1 GLU A 164 " model vdw 2.183 2.440 nonbonded pdb=" OG SER N 69 " pdb=" O THR N 72 " model vdw 2.208 2.440 nonbonded pdb=" NH2 ARG K 456 " pdb=" OE1 GLU K 466 " model vdw 2.208 2.520 nonbonded pdb=" O TRP B 571 " pdb=" NE2 GLN B 575 " model vdw 2.219 2.520 ... (remaining 154238 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 'E' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.760 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 53.650 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.006 0.137 20374 Z= 0.385 Angle : 0.979 19.105 27699 Z= 0.500 Chirality : 0.054 0.311 3301 Planarity : 0.007 0.260 3441 Dihedral : 17.303 112.199 8360 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.89 (0.17), residues: 2442 helix: -1.35 (0.24), residues: 429 sheet: -1.32 (0.21), residues: 615 loop : -1.13 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 427 HIS 0.008 0.002 HIS E 330 PHE 0.034 0.002 PHE I 64 TYR 0.045 0.002 TYR M 116 ARG 0.012 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 745 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7681 (ptpt) cc_final: 0.7303 (ttmm) REVERT: A 217 TYR cc_start: 0.7582 (m-80) cc_final: 0.7155 (m-80) REVERT: B 607 ASN cc_start: 0.8372 (p0) cc_final: 0.8158 (p0) REVERT: B 659 ASP cc_start: 0.8091 (m-30) cc_final: 0.7824 (m-30) REVERT: C 91 THR cc_start: 0.8163 (m) cc_final: 0.7946 (t) REVERT: D 25 THR cc_start: 0.8366 (t) cc_final: 0.8121 (p) REVERT: D 35 VAL cc_start: 0.9009 (t) cc_final: 0.8786 (p) REVERT: D 71 ASN cc_start: 0.7594 (m-40) cc_final: 0.7385 (t0) REVERT: D 89 TYR cc_start: 0.8125 (m-80) cc_final: 0.7534 (m-80) REVERT: E 104 MET cc_start: 0.9010 (ttt) cc_final: 0.8787 (ttp) REVERT: E 121 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7270 (ttmm) REVERT: E 201 CYS cc_start: 0.5711 (m) cc_final: 0.4403 (m) REVERT: E 217 TYR cc_start: 0.7678 (m-80) cc_final: 0.7421 (m-80) REVERT: F 534 SER cc_start: 0.9393 (t) cc_final: 0.9150 (p) REVERT: F 602 LEU cc_start: 0.8622 (pt) cc_final: 0.8336 (pp) REVERT: F 610 TRP cc_start: 0.8454 (t-100) cc_final: 0.8078 (t-100) REVERT: H 101 TRP cc_start: 0.8527 (t60) cc_final: 0.8320 (t-100) REVERT: I 35 VAL cc_start: 0.9046 (t) cc_final: 0.8834 (p) REVERT: I 77 ILE cc_start: 0.8766 (mt) cc_final: 0.8425 (mt) REVERT: I 89 TYR cc_start: 0.8214 (m-80) cc_final: 0.7429 (m-80) REVERT: K 121 LYS cc_start: 0.7643 (ptpt) cc_final: 0.7292 (ttmm) REVERT: L 534 SER cc_start: 0.9418 (t) cc_final: 0.9116 (p) REVERT: L 545 LEU cc_start: 0.6637 (tp) cc_final: 0.6198 (tt) REVERT: L 631 TRP cc_start: 0.8854 (t-100) cc_final: 0.8569 (t-100) REVERT: L 659 ASP cc_start: 0.7798 (m-30) cc_final: 0.7591 (m-30) REVERT: M 4 LEU cc_start: 0.8512 (mm) cc_final: 0.8236 (mp) REVERT: N 25 THR cc_start: 0.8504 (t) cc_final: 0.8127 (p) REVERT: N 89 TYR cc_start: 0.8135 (m-80) cc_final: 0.7847 (m-80) outliers start: 3 outliers final: 0 residues processed: 745 average time/residue: 0.3382 time to fit residues: 374.0095 Evaluate side-chains 423 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 190 optimal weight: 0.0070 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 328 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN E 195 ASN E 302 ASN E 328 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN F 652 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 591 GLN L 640 GLN M 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20374 Z= 0.229 Angle : 0.759 10.712 27699 Z= 0.377 Chirality : 0.048 0.298 3301 Planarity : 0.004 0.044 3441 Dihedral : 12.600 85.296 3941 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 2.91 % Allowed : 14.30 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.72 (0.17), residues: 2442 helix: -1.26 (0.24), residues: 432 sheet: -1.26 (0.20), residues: 681 loop : -0.94 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.005 0.001 HIS A 105 PHE 0.025 0.002 PHE K 233 TYR 0.025 0.002 TYR M 27 ARG 0.007 0.001 ARG K 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 432 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8213 (ptpp) REVERT: A 114 GLN cc_start: 0.8516 (tp40) cc_final: 0.8114 (tp40) REVERT: A 121 LYS cc_start: 0.7709 (ptpt) cc_final: 0.7249 (ttmm) REVERT: B 591 GLN cc_start: 0.8994 (tm130) cc_final: 0.8764 (tm-30) REVERT: B 602 LEU cc_start: 0.8315 (pt) cc_final: 0.8076 (pp) REVERT: C 11 VAL cc_start: 0.8515 (t) cc_final: 0.8255 (m) REVERT: D 35 VAL cc_start: 0.8987 (t) cc_final: 0.8785 (p) REVERT: E 104 MET cc_start: 0.9064 (ttt) cc_final: 0.8843 (ttp) REVERT: E 121 LYS cc_start: 0.7666 (ptpt) cc_final: 0.7225 (ttmm) REVERT: E 217 TYR cc_start: 0.7962 (m-80) cc_final: 0.7676 (m-80) REVERT: E 475 MET cc_start: 0.8071 (mmm) cc_final: 0.6921 (ptp) REVERT: F 602 LEU cc_start: 0.8470 (pt) cc_final: 0.8235 (pp) REVERT: F 648 GLU cc_start: 0.8204 (pp20) cc_final: 0.7769 (tp30) REVERT: H 11 VAL cc_start: 0.8216 (t) cc_final: 0.7984 (m) REVERT: H 101 TRP cc_start: 0.8558 (t60) cc_final: 0.8325 (t-100) REVERT: K 121 LYS cc_start: 0.7819 (ptpt) cc_final: 0.7503 (ttmm) REVERT: K 426 MET cc_start: 0.7083 (pmm) cc_final: 0.5990 (pmm) REVERT: L 542 ARG cc_start: 0.8572 (mtp-110) cc_final: 0.8157 (mtp-110) REVERT: L 622 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6941 (tt) REVERT: M 12 LYS cc_start: 0.7965 (mmmm) cc_final: 0.7652 (mmtp) outliers start: 62 outliers final: 40 residues processed: 463 average time/residue: 0.3336 time to fit residues: 231.8498 Evaluate side-chains 417 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 376 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 347 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 620 SER Chi-restraints excluded: chain L residue 622 ILE Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 221 optimal weight: 30.0000 chunk 238 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN K 105 HIS K 350 GLN ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20374 Z= 0.272 Angle : 0.712 10.500 27699 Z= 0.355 Chirality : 0.047 0.321 3301 Planarity : 0.004 0.037 3441 Dihedral : 10.131 79.591 3941 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 4.03 % Allowed : 16.27 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -1.47 (0.17), residues: 2442 helix: -0.87 (0.25), residues: 432 sheet: -0.85 (0.20), residues: 690 loop : -1.00 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 101 HIS 0.005 0.001 HIS K 330 PHE 0.016 0.002 PHE K 317 TYR 0.016 0.002 TYR N 89 ARG 0.007 0.001 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 414 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8290 (ptpp) REVERT: A 121 LYS cc_start: 0.7743 (ptpt) cc_final: 0.7528 (ttmm) REVERT: A 201 CYS cc_start: 0.6015 (m) cc_final: 0.5792 (m) REVERT: B 646 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.9001 (mm) REVERT: B 653 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 11 VAL cc_start: 0.8587 (t) cc_final: 0.8356 (m) REVERT: C 48 MET cc_start: 0.7580 (mmm) cc_final: 0.7126 (mmm) REVERT: D 71 ASN cc_start: 0.8739 (m-40) cc_final: 0.8331 (t0) REVERT: D 75 LEU cc_start: 0.8695 (tp) cc_final: 0.8462 (tp) REVERT: E 33 ASN cc_start: 0.7371 (p0) cc_final: 0.6946 (p0) REVERT: E 46 LYS cc_start: 0.7994 (mmpt) cc_final: 0.7373 (mttp) REVERT: E 104 MET cc_start: 0.9073 (ttt) cc_final: 0.8858 (ttp) REVERT: E 121 LYS cc_start: 0.7889 (ptpt) cc_final: 0.7662 (ttmm) REVERT: E 217 TYR cc_start: 0.8045 (m-80) cc_final: 0.7613 (m-80) REVERT: E 475 MET cc_start: 0.8227 (mmm) cc_final: 0.6776 (ptp) REVERT: E 502 LYS cc_start: 0.8496 (tptp) cc_final: 0.8276 (tptp) REVERT: F 602 LEU cc_start: 0.8765 (pt) cc_final: 0.8418 (pp) REVERT: F 633 LYS cc_start: 0.8779 (tmmt) cc_final: 0.8527 (ptmt) REVERT: H 11 VAL cc_start: 0.8334 (t) cc_final: 0.7929 (m) REVERT: H 80 TYR cc_start: 0.7731 (m-10) cc_final: 0.7130 (m-10) REVERT: H 101 TRP cc_start: 0.8644 (t60) cc_final: 0.8362 (t-100) REVERT: I 48 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8681 (pp) REVERT: K 121 LYS cc_start: 0.7864 (ptpt) cc_final: 0.7506 (ttmm) REVERT: K 268 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7923 (mmmm) REVERT: K 377 ASN cc_start: 0.8856 (t0) cc_final: 0.8599 (t0) REVERT: K 426 MET cc_start: 0.6699 (pmm) cc_final: 0.6446 (pmm) REVERT: L 542 ARG cc_start: 0.8652 (mtp-110) cc_final: 0.8261 (mtp-110) REVERT: L 648 GLU cc_start: 0.8105 (pp20) cc_final: 0.7883 (tp30) REVERT: M 6 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: M 111 TYR cc_start: 0.9056 (m-80) cc_final: 0.8844 (m-80) outliers start: 86 outliers final: 53 residues processed: 460 average time/residue: 0.3135 time to fit residues: 221.3811 Evaluate side-chains 424 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 368 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 627 THR Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 234 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 591 GLN L 640 GLN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20374 Z= 0.182 Angle : 0.662 13.775 27699 Z= 0.325 Chirality : 0.045 0.324 3301 Planarity : 0.003 0.033 3441 Dihedral : 8.908 70.999 3941 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 3.80 % Allowed : 17.53 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.27 (0.17), residues: 2442 helix: -0.60 (0.26), residues: 432 sheet: -0.63 (0.20), residues: 687 loop : -0.97 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 35 HIS 0.004 0.001 HIS A 105 PHE 0.017 0.001 PHE M 64 TYR 0.016 0.001 TYR M 27 ARG 0.006 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 386 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8283 (ptpp) REVERT: A 121 LYS cc_start: 0.7594 (ptpt) cc_final: 0.7386 (ttmm) REVERT: A 268 LYS cc_start: 0.8473 (mmtp) cc_final: 0.7913 (mmmm) REVERT: C 48 MET cc_start: 0.7565 (mmm) cc_final: 0.7120 (mmm) REVERT: D 71 ASN cc_start: 0.8756 (m-40) cc_final: 0.8367 (t0) REVERT: D 75 LEU cc_start: 0.8659 (tp) cc_final: 0.8436 (tp) REVERT: E 33 ASN cc_start: 0.7491 (p0) cc_final: 0.7049 (p0) REVERT: E 121 LYS cc_start: 0.7785 (ptpt) cc_final: 0.7505 (ttmm) REVERT: E 202 THR cc_start: 0.8993 (p) cc_final: 0.8634 (p) REVERT: E 217 TYR cc_start: 0.8017 (m-80) cc_final: 0.7655 (m-80) REVERT: E 475 MET cc_start: 0.8162 (mmm) cc_final: 0.6688 (ptp) REVERT: E 502 LYS cc_start: 0.8643 (tptp) cc_final: 0.7873 (tttm) REVERT: F 648 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7845 (tp30) REVERT: H 101 TRP cc_start: 0.8652 (t60) cc_final: 0.8371 (t-100) REVERT: I 71 ASN cc_start: 0.8537 (t0) cc_final: 0.8134 (t0) REVERT: K 33 ASN cc_start: 0.7371 (p0) cc_final: 0.7051 (p0) REVERT: K 121 LYS cc_start: 0.7724 (ptpt) cc_final: 0.7241 (ttmm) REVERT: K 217 TYR cc_start: 0.7859 (m-80) cc_final: 0.7185 (m-80) REVERT: K 377 ASN cc_start: 0.8833 (t0) cc_final: 0.8475 (t0) REVERT: K 502 LYS cc_start: 0.7484 (tptp) cc_final: 0.7110 (tptp) REVERT: L 542 ARG cc_start: 0.8610 (mtp-110) cc_final: 0.8222 (mtp-110) REVERT: L 595 ILE cc_start: 0.8614 (mt) cc_final: 0.8400 (mt) REVERT: L 648 GLU cc_start: 0.8126 (pp20) cc_final: 0.7893 (tp30) REVERT: L 653 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8148 (tm-30) REVERT: M 6 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7158 (pt0) outliers start: 81 outliers final: 50 residues processed: 429 average time/residue: 0.3201 time to fit residues: 211.2716 Evaluate side-chains 418 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 367 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 640 GLN Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 659 ASP Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.0270 chunk 210 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 607 ASN ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20374 Z= 0.240 Angle : 0.672 10.090 27699 Z= 0.329 Chirality : 0.046 0.316 3301 Planarity : 0.004 0.032 3441 Dihedral : 8.499 67.562 3941 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.17 % Allowed : 17.91 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -1.21 (0.17), residues: 2442 helix: -0.50 (0.26), residues: 429 sheet: -0.49 (0.20), residues: 693 loop : -1.02 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 427 HIS 0.004 0.001 HIS A 330 PHE 0.023 0.002 PHE F 522 TYR 0.025 0.001 TYR M 106 ARG 0.006 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 374 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8304 (ptpp) REVERT: A 121 LYS cc_start: 0.7682 (ptpt) cc_final: 0.7477 (ttmm) REVERT: B 535 MET cc_start: 0.7694 (mmm) cc_final: 0.7406 (mpp) REVERT: C 48 MET cc_start: 0.7618 (mmm) cc_final: 0.7215 (mmm) REVERT: E 33 ASN cc_start: 0.7388 (p0) cc_final: 0.6942 (p0) REVERT: E 202 THR cc_start: 0.9055 (p) cc_final: 0.8726 (p) REVERT: F 633 LYS cc_start: 0.8734 (tmmt) cc_final: 0.8465 (ptmt) REVERT: F 650 GLN cc_start: 0.8878 (tp40) cc_final: 0.8015 (tm-30) REVERT: H 101 TRP cc_start: 0.8663 (t60) cc_final: 0.8343 (t-100) REVERT: I 90 CYS cc_start: 0.5819 (p) cc_final: 0.5136 (p) REVERT: K 33 ASN cc_start: 0.7525 (p0) cc_final: 0.7098 (p0) REVERT: K 121 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7489 (ttmm) REVERT: K 217 TYR cc_start: 0.7931 (m-80) cc_final: 0.7247 (m-80) REVERT: K 377 ASN cc_start: 0.8856 (t0) cc_final: 0.8471 (t0) REVERT: K 502 LYS cc_start: 0.7723 (tptp) cc_final: 0.7299 (tptp) REVERT: L 542 ARG cc_start: 0.8501 (mtp-110) cc_final: 0.8160 (mtp-110) REVERT: L 653 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8292 (tm-30) REVERT: M 6 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: M 46 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7833 (mm-30) REVERT: N 55 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8114 (mtpp) outliers start: 89 outliers final: 61 residues processed: 417 average time/residue: 0.3172 time to fit residues: 204.6075 Evaluate side-chains 418 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 356 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain L residue 535 MET Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 640 GLN Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 195 optimal weight: 0.0270 chunk 108 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 overall best weight: 3.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 62 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 575 GLN L 640 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20374 Z= 0.268 Angle : 0.681 10.145 27699 Z= 0.331 Chirality : 0.046 0.312 3301 Planarity : 0.004 0.036 3441 Dihedral : 8.240 63.882 3941 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.72 % Rotamer: Outliers : 4.64 % Allowed : 18.80 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -1.24 (0.17), residues: 2442 helix: -0.46 (0.27), residues: 429 sheet: -0.48 (0.20), residues: 696 loop : -1.09 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS A 330 PHE 0.013 0.002 PHE L 522 TYR 0.019 0.002 TYR M 106 ARG 0.006 0.001 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 371 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7859 (ptpt) cc_final: 0.7599 (ttmm) REVERT: E 33 ASN cc_start: 0.7534 (p0) cc_final: 0.7095 (p0) REVERT: E 202 THR cc_start: 0.9127 (p) cc_final: 0.8786 (p) REVERT: E 475 MET cc_start: 0.7962 (mmm) cc_final: 0.6701 (ptp) REVERT: F 633 LYS cc_start: 0.8731 (tmmt) cc_final: 0.8478 (ptmt) REVERT: F 650 GLN cc_start: 0.8980 (tp40) cc_final: 0.8023 (tm-30) REVERT: H 101 TRP cc_start: 0.8698 (t60) cc_final: 0.8338 (t-100) REVERT: K 33 ASN cc_start: 0.7314 (p0) cc_final: 0.6866 (p0) REVERT: K 121 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7672 (ttmm) REVERT: K 217 TYR cc_start: 0.8014 (m-80) cc_final: 0.7375 (m-80) REVERT: K 377 ASN cc_start: 0.8904 (t0) cc_final: 0.8496 (t0) REVERT: K 425 ASN cc_start: 0.7677 (m-40) cc_final: 0.6910 (p0) REVERT: K 502 LYS cc_start: 0.7881 (tptp) cc_final: 0.7541 (tptp) REVERT: L 542 ARG cc_start: 0.8548 (mtp-110) cc_final: 0.8162 (mtp-110) REVERT: M 6 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7369 (pt0) outliers start: 99 outliers final: 73 residues processed: 416 average time/residue: 0.3092 time to fit residues: 199.1211 Evaluate side-chains 427 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 353 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 640 GLN Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 659 ASP Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 92 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 197 optimal weight: 0.0020 chunk 131 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20374 Z= 0.165 Angle : 0.653 10.315 27699 Z= 0.315 Chirality : 0.045 0.314 3301 Planarity : 0.003 0.038 3441 Dihedral : 7.723 58.546 3941 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 3.14 % Allowed : 20.82 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -1.09 (0.18), residues: 2442 helix: -0.34 (0.27), residues: 429 sheet: -0.40 (0.20), residues: 708 loop : -0.98 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.004 0.001 HIS A 105 PHE 0.020 0.001 PHE L 522 TYR 0.017 0.001 TYR M 106 ARG 0.006 0.000 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 380 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7653 (ptpt) cc_final: 0.7448 (ttmm) REVERT: C 10 GLU cc_start: 0.7554 (tp30) cc_final: 0.7260 (tp30) REVERT: D 23 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8295 (p) REVERT: E 33 ASN cc_start: 0.7553 (p0) cc_final: 0.7148 (p0) REVERT: E 202 THR cc_start: 0.9037 (p) cc_final: 0.8691 (p) REVERT: E 475 MET cc_start: 0.7596 (mmm) cc_final: 0.6659 (ptp) REVERT: F 648 GLU cc_start: 0.8124 (pp20) cc_final: 0.7782 (tp30) REVERT: F 650 GLN cc_start: 0.8881 (tp40) cc_final: 0.8078 (tm-30) REVERT: H 101 TRP cc_start: 0.8659 (t60) cc_final: 0.8330 (t-100) REVERT: I 71 ASN cc_start: 0.8719 (t0) cc_final: 0.8034 (t0) REVERT: K 33 ASN cc_start: 0.7337 (p0) cc_final: 0.6869 (p0) REVERT: K 121 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7522 (ttmm) REVERT: K 217 TYR cc_start: 0.8015 (m-80) cc_final: 0.7311 (m-80) REVERT: K 377 ASN cc_start: 0.8955 (t0) cc_final: 0.8514 (t0) REVERT: K 502 LYS cc_start: 0.7822 (tptp) cc_final: 0.7537 (tptp) REVERT: L 542 ARG cc_start: 0.8535 (mtp-110) cc_final: 0.8139 (mtp-110) REVERT: M 46 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7818 (mm-30) REVERT: N 55 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8248 (mtpp) REVERT: N 75 LEU cc_start: 0.8635 (tp) cc_final: 0.8346 (tt) outliers start: 67 outliers final: 47 residues processed: 412 average time/residue: 0.3134 time to fit residues: 199.5163 Evaluate side-chains 412 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 364 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 350 GLN Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 659 ASP Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS L 543 ASN M 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20374 Z= 0.235 Angle : 0.670 11.488 27699 Z= 0.323 Chirality : 0.045 0.308 3301 Planarity : 0.004 0.038 3441 Dihedral : 7.631 57.857 3941 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 3.09 % Allowed : 21.33 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2442 helix: -0.10 (0.27), residues: 411 sheet: -0.32 (0.20), residues: 699 loop : -1.01 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 628 HIS 0.003 0.001 HIS A 105 PHE 0.011 0.001 PHE A 317 TYR 0.017 0.001 TYR M 106 ARG 0.005 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 370 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7862 (ptpt) cc_final: 0.7594 (ttmm) REVERT: A 164 GLU cc_start: 0.7311 (pm20) cc_final: 0.7001 (pt0) REVERT: C 10 GLU cc_start: 0.7596 (tp30) cc_final: 0.6768 (mm-30) REVERT: E 33 ASN cc_start: 0.7640 (p0) cc_final: 0.7244 (p0) REVERT: E 202 THR cc_start: 0.9107 (p) cc_final: 0.8769 (p) REVERT: E 475 MET cc_start: 0.7797 (mmm) cc_final: 0.6747 (ptp) REVERT: F 648 GLU cc_start: 0.8097 (pp20) cc_final: 0.7750 (tp30) REVERT: F 650 GLN cc_start: 0.8904 (tp40) cc_final: 0.8026 (tm-30) REVERT: H 101 TRP cc_start: 0.8680 (t60) cc_final: 0.8297 (t-100) REVERT: K 33 ASN cc_start: 0.7378 (p0) cc_final: 0.6959 (p0) REVERT: K 121 LYS cc_start: 0.8157 (ptpt) cc_final: 0.7713 (ttmm) REVERT: K 217 TYR cc_start: 0.7913 (m-80) cc_final: 0.7328 (m-80) REVERT: K 371 ILE cc_start: 0.8792 (tp) cc_final: 0.8585 (tt) REVERT: K 377 ASN cc_start: 0.8967 (t0) cc_final: 0.8492 (t0) REVERT: K 502 LYS cc_start: 0.8108 (tptp) cc_final: 0.7746 (tptp) REVERT: L 542 ARG cc_start: 0.8514 (mtp-110) cc_final: 0.8065 (mtp-110) REVERT: M 6 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: N 55 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8369 (mtpp) outliers start: 66 outliers final: 53 residues processed: 404 average time/residue: 0.3060 time to fit residues: 191.1438 Evaluate side-chains 415 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 361 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 350 GLN Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 659 ASP Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 206 optimal weight: 0.5980 chunk 217 optimal weight: 0.0870 chunk 143 optimal weight: 8.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN E 105 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 ASN M 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20374 Z= 0.164 Angle : 0.663 12.089 27699 Z= 0.318 Chirality : 0.045 0.310 3301 Planarity : 0.003 0.037 3441 Dihedral : 7.176 56.440 3941 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.67 % Favored : 95.21 % Rotamer: Outliers : 2.58 % Allowed : 22.46 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -0.86 (0.18), residues: 2442 helix: -0.05 (0.27), residues: 411 sheet: -0.19 (0.20), residues: 702 loop : -0.91 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 628 HIS 0.004 0.001 HIS K 374 PHE 0.011 0.001 PHE M 64 TYR 0.017 0.001 TYR M 27 ARG 0.005 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 371 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7561 (p0) cc_final: 0.7083 (p0) REVERT: A 121 LYS cc_start: 0.7623 (ptpt) cc_final: 0.7366 (ttmm) REVERT: A 164 GLU cc_start: 0.7266 (pm20) cc_final: 0.6975 (pt0) REVERT: B 602 LEU cc_start: 0.8286 (pt) cc_final: 0.7865 (pp) REVERT: C 10 GLU cc_start: 0.7558 (tp30) cc_final: 0.6964 (mm-30) REVERT: E 33 ASN cc_start: 0.7615 (p0) cc_final: 0.7195 (p0) REVERT: E 202 THR cc_start: 0.9032 (p) cc_final: 0.8691 (p) REVERT: F 622 ILE cc_start: 0.7017 (tp) cc_final: 0.6785 (tp) REVERT: F 648 GLU cc_start: 0.8078 (pp20) cc_final: 0.7780 (tp30) REVERT: F 650 GLN cc_start: 0.8830 (tp40) cc_final: 0.8096 (tm-30) REVERT: H 10 GLU cc_start: 0.8163 (tp30) cc_final: 0.7769 (mm-30) REVERT: H 101 TRP cc_start: 0.8629 (t60) cc_final: 0.8268 (t-100) REVERT: K 33 ASN cc_start: 0.7382 (p0) cc_final: 0.6963 (p0) REVERT: K 121 LYS cc_start: 0.8023 (ptpt) cc_final: 0.7505 (ttmm) REVERT: K 217 TYR cc_start: 0.7854 (m-80) cc_final: 0.7217 (m-80) REVERT: K 377 ASN cc_start: 0.9001 (t0) cc_final: 0.8527 (t0) REVERT: K 502 LYS cc_start: 0.8019 (tptp) cc_final: 0.7747 (tptp) REVERT: L 542 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.8112 (mtp-110) REVERT: M 6 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: M 46 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7875 (mm-30) REVERT: N 55 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8494 (mtpp) outliers start: 55 outliers final: 43 residues processed: 401 average time/residue: 0.3157 time to fit residues: 195.0129 Evaluate side-chains 403 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 359 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 350 GLN Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 659 ASP Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 148 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 ASN K 105 HIS M 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20374 Z= 0.295 Angle : 0.709 12.063 27699 Z= 0.342 Chirality : 0.046 0.302 3301 Planarity : 0.004 0.036 3441 Dihedral : 7.407 57.199 3941 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 3.14 % Allowed : 21.85 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -0.97 (0.18), residues: 2442 helix: -0.15 (0.27), residues: 411 sheet: -0.28 (0.20), residues: 711 loop : -0.97 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 628 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.002 PHE A 317 TYR 0.018 0.002 TYR H 80 ARG 0.009 0.001 ARG H 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 368 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7748 (p0) cc_final: 0.7291 (p0) REVERT: A 121 LYS cc_start: 0.7963 (ptpt) cc_final: 0.7674 (ttmm) REVERT: C 48 MET cc_start: 0.7751 (mmm) cc_final: 0.7508 (mtt) REVERT: E 33 ASN cc_start: 0.7565 (p0) cc_final: 0.7215 (p0) REVERT: E 202 THR cc_start: 0.9147 (p) cc_final: 0.8834 (p) REVERT: F 622 ILE cc_start: 0.7176 (tp) cc_final: 0.6946 (tp) REVERT: F 646 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8843 (mm) REVERT: F 648 GLU cc_start: 0.8113 (pp20) cc_final: 0.7717 (tp30) REVERT: F 650 GLN cc_start: 0.8883 (tp40) cc_final: 0.7971 (tm-30) REVERT: H 10 GLU cc_start: 0.8308 (tp30) cc_final: 0.7855 (mm-30) REVERT: K 33 ASN cc_start: 0.7453 (p0) cc_final: 0.7084 (p0) REVERT: K 121 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7742 (ttmm) REVERT: K 164 GLU cc_start: 0.7091 (pm20) cc_final: 0.6694 (pm20) REVERT: K 217 TYR cc_start: 0.8025 (m-80) cc_final: 0.7468 (m-80) REVERT: K 268 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8243 (mmmm) REVERT: K 377 ASN cc_start: 0.9016 (t0) cc_final: 0.8526 (t0) REVERT: K 502 LYS cc_start: 0.8085 (tptp) cc_final: 0.7740 (tptp) REVERT: L 542 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8151 (mtp-110) REVERT: M 46 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7927 (mm-30) REVERT: N 23 THR cc_start: 0.8878 (p) cc_final: 0.8613 (p) REVERT: N 55 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8509 (mtpp) outliers start: 67 outliers final: 52 residues processed: 401 average time/residue: 0.3141 time to fit residues: 193.6781 Evaluate side-chains 409 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 356 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 350 GLN Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 62 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 177 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 198 optimal weight: 50.0000 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102315 restraints weight = 37383.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101327 restraints weight = 32252.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102593 restraints weight = 32963.087| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20374 Z= 0.165 Angle : 0.670 12.228 27699 Z= 0.320 Chirality : 0.045 0.305 3301 Planarity : 0.003 0.036 3441 Dihedral : 6.904 56.367 3941 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.09 % Rotamer: Outliers : 2.30 % Allowed : 23.30 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.25 % 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: -0.81 (0.18), residues: 2442 helix: -0.04 (0.27), residues: 411 sheet: -0.18 (0.20), residues: 714 loop : -0.85 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 628 HIS 0.004 0.001 HIS K 374 PHE 0.010 0.001 PHE M 64 TYR 0.015 0.001 TYR M 27 ARG 0.005 0.000 ARG E 503 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.84 seconds wall clock time: 81 minutes 23.58 seconds (4883.58 seconds total)