Starting phenix.real_space_refine on Fri Feb 16 18:28:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/02_2024/7l8x_23239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/02_2024/7l8x_23239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/02_2024/7l8x_23239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/02_2024/7l8x_23239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/02_2024/7l8x_23239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/02_2024/7l8x_23239_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.003 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 104 5.16 5 C 10010 2.51 5 N 2703 2.21 5 O 3273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16090 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3507 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 2 Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1155 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "C" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3461 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "E" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3371 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "F" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1101 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 2, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.21, per 1000 atoms: 0.57 Number of scatterers: 16090 At special positions: 0 Unit cell: (129.78, 128.75, 122.57, 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 104 16.00 O 3273 8.00 N 2703 7.00 C 10010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN T 4 " - " MAN T 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 9 " " BMA T 3 " - " MAN T 6 " " BMA b 3 " - " MAN b 6 " BETA1-3 " MAN K 7 " - " BMA K 8 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 160 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 133 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 289 " " NAG A 614 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 448 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 160 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 289 " " NAG C 612 " - " ASN C 363 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 448 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 156 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 133 " " NAG E 610 " - " ASN E 355 " " NAG E 611 " - " ASN E 289 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 392 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN B 611 " " NAG O 1 " - " ASN C 88 " " NAG P 1 " - " ASN C 392 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 332 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN D 611 " " NAG W 1 " - " ASN E 88 " " NAG X 1 " - " ASN E 392 " " NAG Y 1 " - " ASN E 386 " " NAG Z 1 " - " ASN E 332 " " NAG a 1 " - " ASN E 295 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 197 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN F 611 " Time building additional restraints: 8.02 Conformation dependent library (CDL) restraints added in 2.5 seconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 34 sheets defined 28.2% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.417A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 352 removed outlier: 4.211A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 5.042A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.336A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 530 through 544 removed outlier: 4.033A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 removed outlier: 3.592A pdb=" N LEU B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 removed outlier: 3.584A pdb=" N LEU B 566 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 663 removed outlier: 5.193A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.023A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 475 through 485 removed outlier: 4.494A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 527 removed outlier: 4.197A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 532 through 543 removed outlier: 5.123A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 663 removed outlier: 5.394A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 657 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'E' and resid 101 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 352 removed outlier: 4.161A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 378 through 380 No H-bonds generated for 'chain 'E' and resid 378 through 380' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 475 through 482 removed outlier: 3.753A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.405A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 532 through 534 No H-bonds generated for 'chain 'F' and resid 532 through 534' Processing helix chain 'F' and resid 537 through 556 removed outlier: 4.161A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 567 No H-bonds generated for 'chain 'F' and resid 565 through 567' Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 619 through 623 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 656 removed outlier: 5.126A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.551A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= I, first strand: chain 'A' and resid 443 through 449 removed outlier: 4.044A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.485A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.421A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'C' and resid 52 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= P, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= R, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.326A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 443 through 448 removed outlier: 4.104A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 304 through 309 Processing sheet with id= U, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= V, first strand: chain 'H' and resid 113 through 115 removed outlier: 6.165A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N UNK H 50 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= X, first strand: chain 'L' and resid 81 through 86 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= Z, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.532A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AB, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= AC, first strand: chain 'E' and resid 130 through 132 Processing sheet with id= AD, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AE, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= AF, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.407A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 374 through 376 removed outlier: 4.288A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.754A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.08 Time building geometry restraints manager: 8.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3151 1.32 - 1.45: 5158 1.45 - 1.59: 7855 1.59 - 1.73: 62 1.73 - 1.87: 133 Bond restraints: 16359 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.45e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.30e+01 bond pdb=" CB HIS E 105 " pdb=" CG HIS E 105 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.09e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 16354 not shown) Histogram of bond angle deviations from ideal: 94.53 - 102.62: 113 102.62 - 110.72: 6195 110.72 - 118.81: 7797 118.81 - 126.91: 7904 126.91 - 135.00: 240 Bond angle restraints: 22249 Sorted by residual: angle pdb=" N MET E 100 " pdb=" CA MET E 100 " pdb=" C MET E 100 " ideal model delta sigma weight residual 114.62 100.33 14.29 1.14e+00 7.69e-01 1.57e+02 angle pdb=" N THR C 464 " pdb=" CA THR C 464 " pdb=" C THR C 464 " ideal model delta sigma weight residual 114.56 102.88 11.68 1.27e+00 6.20e-01 8.46e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.87 -8.31 1.02e+00 9.61e-01 6.64e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.01e+00 9.80e-01 6.20e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.01e+00 9.80e-01 6.09e+01 ... (remaining 22244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 10814 21.15 - 42.30: 236 42.30 - 63.45: 78 63.45 - 84.60: 39 84.60 - 105.75: 22 Dihedral angle restraints: 11189 sinusoidal: 5573 harmonic: 5616 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.43 -67.43 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.41 -60.41 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS E 74 " pdb=" SG CYS E 74 " pdb=" SG CYS F 561 " pdb=" CB CYS F 561 " ideal model delta sinusoidal sigma weight residual 93.00 46.11 46.89 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 11186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2748 0.329 - 0.657: 122 0.657 - 0.986: 0 0.986 - 1.314: 0 1.314 - 1.643: 1 Chirality restraints: 2871 Sorted by residual: chirality pdb=" C1 MAN K 7 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 7 " pdb=" O5 MAN K 7 " both_signs ideal model delta sigma weight residual False 2.40 0.76 1.64 2.00e-02 2.50e+03 6.75e+03 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.74e+02 ... (remaining 2868 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG Z 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.113 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.348 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C 604 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.335 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG K 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.103 2.00e-02 2.50e+03 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3720 2.80 - 3.33: 15066 3.33 - 3.85: 25588 3.85 - 4.38: 30591 4.38 - 4.90: 48376 Nonbonded interactions: 123341 Sorted by model distance: nonbonded pdb=" O3 NAG A 605 " pdb=" O7 NAG A 605 " model vdw 2.275 2.440 nonbonded pdb=" O3 NAG C 602 " pdb=" O7 NAG C 602 " model vdw 2.324 2.440 nonbonded pdb=" N HIS A 72 " pdb=" O HIS A 72 " model vdw 2.345 2.496 nonbonded pdb=" N GLY D 597 " pdb=" O GLY D 597 " model vdw 2.393 2.496 nonbonded pdb=" N MET E 100 " pdb=" N VAL E 101 " model vdw 2.406 2.560 ... (remaining 123336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 60 or resid 66 through 162 or resid 170 through \ 185 or resid 189 through 457 or resid 462 through 503 or resid 601 through 611) \ ) selection = (chain 'C' and (resid 33 through 162 or resid 170 through 185 or resid 189 throu \ gh 457 or resid 462 through 503 or resid 601 through 611)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 564 through 657 or resid 701)) selection = (chain 'D' and (resid 520 through 657 or resid 701)) selection = (chain 'F' and (resid 520 through 546 or resid 564 through 657 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'H' and resid 19 through 117) selection = chain 'L' } ncs_group { reference = chain 'T' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.950 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.950 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.022 0.144 16359 Z= 1.356 Angle : 1.697 14.290 22249 Z= 1.092 Chirality : 0.141 1.643 2871 Planarity : 0.018 0.300 2708 Dihedral : 11.797 105.749 7431 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1687 helix: 0.58 (0.23), residues: 436 sheet: 0.78 (0.25), residues: 393 loop : 0.78 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.010 TRP B 571 HIS 0.008 0.002 HIS E 374 PHE 0.031 0.006 PHE E 353 TYR 0.060 0.008 TYR C 40 ARG 0.009 0.001 ARG F 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 1.837 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: B 568 LEU cc_start: 0.7830 (tp) cc_final: 0.7623 (tt) outliers start: 0 outliers final: 2 residues processed: 492 average time/residue: 1.1788 time to fit residues: 646.6102 Evaluate side-chains 203 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain D residue 573 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 575 GLN B 658 GLN C 33 ASN C 105 HIS C 114 GLN C 377 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 577 GLN D 651 ASN E 85 HIS E 99 ASN E 130 GLN E 195 ASN F 554 ASN F 591 GLN F 625 ASN F 630 GLN F 640 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16359 Z= 0.244 Angle : 0.766 9.932 22249 Z= 0.382 Chirality : 0.049 0.541 2871 Planarity : 0.005 0.042 2708 Dihedral : 9.323 88.126 4173 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.36 % Allowed : 15.15 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1687 helix: 1.28 (0.24), residues: 418 sheet: 0.65 (0.22), residues: 468 loop : 0.36 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 610 HIS 0.004 0.001 HIS E 374 PHE 0.024 0.002 PHE E 383 TYR 0.022 0.002 TYR E 173 ARG 0.009 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 274 time to evaluate : 1.862 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: B 623 TRP cc_start: 0.6058 (OUTLIER) cc_final: 0.5212 (m100) REVERT: F 529 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8180 (m) outliers start: 82 outliers final: 29 residues processed: 322 average time/residue: 1.0368 time to fit residues: 376.6352 Evaluate side-chains 219 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 98 ASN D 577 GLN E 33 ASN E 99 ASN F 554 ASN F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16359 Z= 0.246 Angle : 0.675 8.079 22249 Z= 0.338 Chirality : 0.046 0.293 2871 Planarity : 0.004 0.042 2708 Dihedral : 8.132 81.449 4173 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.16 % Allowed : 18.29 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1687 helix: 0.99 (0.26), residues: 420 sheet: 0.67 (0.22), residues: 477 loop : 0.23 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 610 HIS 0.005 0.001 HIS E 374 PHE 0.020 0.002 PHE E 383 TYR 0.017 0.002 TYR E 486 ARG 0.008 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 232 time to evaluate : 2.126 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: B 623 TRP cc_start: 0.6244 (OUTLIER) cc_final: 0.5352 (m100) REVERT: F 529 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8244 (m) outliers start: 79 outliers final: 38 residues processed: 281 average time/residue: 1.0253 time to fit residues: 326.3435 Evaluate side-chains 223 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 649 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.3980 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN C 33 ASN C 425 ASN D 577 GLN D 591 GLN E 99 ASN E 425 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16359 Z= 0.191 Angle : 0.647 10.759 22249 Z= 0.323 Chirality : 0.045 0.291 2871 Planarity : 0.004 0.047 2708 Dihedral : 7.133 75.512 4169 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 4.83 % Allowed : 19.33 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1687 helix: 1.01 (0.26), residues: 405 sheet: 0.64 (0.22), residues: 466 loop : -0.08 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 610 HIS 0.005 0.001 HIS E 374 PHE 0.018 0.002 PHE E 383 TYR 0.023 0.002 TYR E 173 ARG 0.009 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 227 time to evaluate : 1.892 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: B 623 TRP cc_start: 0.6314 (OUTLIER) cc_final: 0.5390 (m100) REVERT: C 308 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6653 (ttp80) REVERT: D 579 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7811 (mtt-85) outliers start: 74 outliers final: 32 residues processed: 278 average time/residue: 1.0784 time to fit residues: 337.6851 Evaluate side-chains 225 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 617 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 0.0670 chunk 155 optimal weight: 0.5980 chunk 125 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN D 577 GLN D 590 GLN E 33 ASN E 99 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16359 Z= 0.369 Angle : 0.742 8.680 22249 Z= 0.369 Chirality : 0.048 0.279 2871 Planarity : 0.005 0.051 2708 Dihedral : 7.343 73.245 4169 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 5.68 % Allowed : 19.40 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1687 helix: 0.97 (0.27), residues: 396 sheet: 0.42 (0.23), residues: 442 loop : -0.29 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 610 HIS 0.008 0.001 HIS E 374 PHE 0.022 0.002 PHE E 383 TYR 0.018 0.002 TYR C 435 ARG 0.010 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 192 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7910 (mptm) REVERT: B 623 TRP cc_start: 0.6424 (OUTLIER) cc_final: 0.5716 (m100) REVERT: D 567 LYS cc_start: 0.7513 (mtmm) cc_final: 0.7283 (mtmm) REVERT: D 568 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6705 (pp) REVERT: E 227 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7389 (ttmm) outliers start: 87 outliers final: 44 residues processed: 258 average time/residue: 1.0802 time to fit residues: 313.7458 Evaluate side-chains 226 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 178 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 620 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 577 GLN D 577 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16359 Z= 0.290 Angle : 0.672 10.260 22249 Z= 0.336 Chirality : 0.045 0.290 2871 Planarity : 0.004 0.052 2708 Dihedral : 7.092 69.273 4169 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 5.29 % Allowed : 21.23 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1687 helix: 0.82 (0.27), residues: 401 sheet: 0.21 (0.23), residues: 459 loop : -0.39 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 395 HIS 0.005 0.001 HIS E 374 PHE 0.016 0.002 PHE A 53 TYR 0.024 0.002 TYR E 173 ARG 0.009 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 202 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7855 (mptm) REVERT: A 499 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7725 (m) REVERT: B 623 TRP cc_start: 0.6422 (OUTLIER) cc_final: 0.5672 (m100) REVERT: C 316 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.7514 (m-90) REVERT: D 568 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6676 (pp) outliers start: 81 outliers final: 47 residues processed: 261 average time/residue: 1.0819 time to fit residues: 317.5047 Evaluate side-chains 230 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 178 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 649 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 328 GLN D 577 GLN D 640 GLN E 33 ASN E 99 ASN E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16359 Z= 0.319 Angle : 0.690 10.195 22249 Z= 0.343 Chirality : 0.046 0.290 2871 Planarity : 0.004 0.052 2708 Dihedral : 7.156 66.991 4169 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 5.23 % Allowed : 21.88 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1687 helix: 0.63 (0.26), residues: 407 sheet: 0.14 (0.24), residues: 427 loop : -0.58 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 69 HIS 0.005 0.001 HIS F 564 PHE 0.017 0.002 PHE A 53 TYR 0.025 0.002 TYR D 643 ARG 0.008 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 189 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7860 (mptm) REVERT: B 623 TRP cc_start: 0.6466 (OUTLIER) cc_final: 0.5774 (m100) REVERT: D 568 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6733 (pp) REVERT: F 562 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7459 (pt0) outliers start: 80 outliers final: 52 residues processed: 248 average time/residue: 1.0377 time to fit residues: 291.7360 Evaluate side-chains 239 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 183 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN D 577 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16359 Z= 0.195 Angle : 0.635 11.591 22249 Z= 0.317 Chirality : 0.044 0.296 2871 Planarity : 0.004 0.053 2708 Dihedral : 6.718 62.052 4169 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 3.85 % Allowed : 23.58 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1687 helix: 0.77 (0.27), residues: 406 sheet: 0.05 (0.23), residues: 444 loop : -0.59 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 395 HIS 0.005 0.001 HIS E 374 PHE 0.016 0.002 PHE E 159 TYR 0.022 0.002 TYR D 643 ARG 0.007 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 623 TRP cc_start: 0.6358 (OUTLIER) cc_final: 0.5559 (m100) outliers start: 59 outliers final: 39 residues processed: 256 average time/residue: 1.1122 time to fit residues: 321.0766 Evaluate side-chains 228 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 649 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN D 577 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16359 Z= 0.206 Angle : 0.651 12.742 22249 Z= 0.323 Chirality : 0.044 0.297 2871 Planarity : 0.004 0.060 2708 Dihedral : 6.438 59.864 4169 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 3.20 % Allowed : 25.21 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1687 helix: 0.79 (0.27), residues: 400 sheet: -0.02 (0.23), residues: 443 loop : -0.54 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 395 HIS 0.005 0.001 HIS E 374 PHE 0.014 0.002 PHE A 53 TYR 0.021 0.002 TYR D 643 ARG 0.015 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 623 TRP cc_start: 0.6281 (OUTLIER) cc_final: 0.5624 (m100) REVERT: B 647 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7936 (tm-30) outliers start: 49 outliers final: 31 residues processed: 237 average time/residue: 1.0935 time to fit residues: 292.1798 Evaluate side-chains 218 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 124 optimal weight: 20.0000 chunk 187 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN D 577 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16359 Z= 0.287 Angle : 0.697 13.046 22249 Z= 0.347 Chirality : 0.045 0.295 2871 Planarity : 0.004 0.050 2708 Dihedral : 6.405 58.186 4169 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 3.07 % Allowed : 25.02 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1687 helix: 0.69 (0.27), residues: 399 sheet: -0.06 (0.23), residues: 451 loop : -0.59 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 395 HIS 0.010 0.001 HIS F 564 PHE 0.015 0.002 PHE A 53 TYR 0.020 0.002 TYR C 486 ARG 0.013 0.001 ARG E 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 194 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 623 TRP cc_start: 0.6417 (OUTLIER) cc_final: 0.5742 (m100) REVERT: B 647 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7874 (tm-30) outliers start: 47 outliers final: 33 residues processed: 228 average time/residue: 1.1294 time to fit residues: 290.5763 Evaluate side-chains 215 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN D 590 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088063 restraints weight = 34375.779| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.29 r_work: 0.3128 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16359 Z= 0.283 Angle : 0.701 12.695 22249 Z= 0.347 Chirality : 0.045 0.291 2871 Planarity : 0.004 0.049 2708 Dihedral : 6.417 56.176 4169 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 3.72 % Allowed : 24.95 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1687 helix: 0.66 (0.27), residues: 399 sheet: -0.14 (0.23), residues: 470 loop : -0.67 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 395 HIS 0.008 0.001 HIS F 564 PHE 0.015 0.002 PHE A 53 TYR 0.036 0.002 TYR D 643 ARG 0.014 0.001 ARG E 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5787.01 seconds wall clock time: 103 minutes 45.05 seconds (6225.05 seconds total)