Starting phenix.real_space_refine on Tue Jul 23 04:57:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4i_41883/07_2024/8u4i_41883_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4i_41883/07_2024/8u4i_41883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4i_41883/07_2024/8u4i_41883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4i_41883/07_2024/8u4i_41883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4i_41883/07_2024/8u4i_41883_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4i_41883/07_2024/8u4i_41883_trim.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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: 5 Type Number sf(0) Gaussians S 132 5.16 5 C 6679 2.51 5 N 1795 2.21 5 O 2235 1.98 5 H 9593 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 544": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 612": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 544": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 612": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20434 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 9093 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 2 Chain: "B" Number of atoms: 9088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9088 Classifications: {'peptide': 600} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 572} Chain breaks: 2 Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 768 Classifications: {'peptide': 50} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "D" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 768 Classifications: {'peptide': 50} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: "B" 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 Time building chain proxies: 11.09, per 1000 atoms: 0.54 Number of scatterers: 20434 At special positions: 0 Unit cell: (85.17, 147.795, 137.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 O 2235 8.00 N 1795 7.00 C 6679 6.00 H 9593 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.13 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.05 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.02 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 229 " distance=2.01 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=2.01 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.11 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 289 " distance=2.11 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.01 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.28 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.10 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.01 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.02 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.06 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.02 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.01 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 56 " distance=2.12 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 197 " distance=2.02 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 221 " distance=2.04 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 229 " distance=2.15 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 238 " distance=2.01 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.20 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 258 " distance=2.08 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 304 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 330 " distance=2.02 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.05 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 496 " distance=2.04 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 512 " distance=1.79 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 552 " distance=2.02 Simple disulfide: pdb=" SG CYS B 555 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 577 " distance=2.04 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 589 " distance=2.05 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 625 " distance=2.02 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 633 " distance=2.08 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 210 " distance=2.13 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 221 " distance=2.02 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 190 " - pdb=" SG CYS D 210 " distance=2.04 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 221 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 701 " - " ASN A 495 " " NAG B 701 " - " ASN B 495 " " NAG E 1 " - " ASN A 548 " " NAG F 1 " - " ASN A 576 " " NAG G 1 " - " ASN A 473 " " NAG H 1 " - " ASN A 253 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 410 " " NAG K 1 " - " ASN A 138 " " NAG L 1 " - " ASN B 138 " " NAG M 1 " - " ASN B 253 " " NAG N 1 " - " ASN B 358 " " NAG O 1 " - " ASN B 410 " " NAG P 1 " - " ASN B 473 " " NAG Q 1 " - " ASN B 548 " " NAG R 1 " - " ASN B 576 " Time building additional restraints: 16.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 17.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.626A pdb=" N SER A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.814A pdb=" N ILE A 161 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.672A pdb=" N CYS A 229 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.937A pdb=" N ILE A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.152A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.607A pdb=" N HIS A 470 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 573 through 577 removed outlier: 4.069A pdb=" N CYS A 577 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 54 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.646A pdb=" N SER B 79 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.673A pdb=" N ILE B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.777A pdb=" N MET B 343 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.014A pdb=" N THR B 394 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.549A pdb=" N HIS B 470 " --> pdb=" O CYS B 467 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 472 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 629 through 633 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.955A pdb=" N CYS C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.099A pdb=" N SER A 38 " --> pdb=" O CYS C 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.602A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A 147 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.761A pdb=" N ALA A 248 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY A 237 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N CYS A 246 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA7, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.949A pdb=" N GLN A 274 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.575A pdb=" N VAL A 298 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AB2, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.397A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 366 through 368 removed outlier: 4.621A pdb=" N LEU A 432 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N TYR A 459 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 434 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR A 461 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 436 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.881A pdb=" N ILE A 531 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 545 through 548 Processing sheet with id=AB6, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AB7, first strand: chain 'A' and resid 606 through 608 Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 39 removed outlier: 4.343A pdb=" N ARG D 207 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.470A pdb=" N GLY B 146 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 117 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AC2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AC3, first strand: chain 'B' and resid 235 through 238 removed outlier: 3.706A pdb=" N ALA B 248 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 237 " --> pdb=" O CYS B 246 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N CYS B 246 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AC5, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.030A pdb=" N GLN B 274 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC7, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC9, first strand: chain 'B' and resid 334 through 335 removed outlier: 7.004A pdb=" N CYS B 334 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 366 through 368 removed outlier: 6.595A pdb=" N LEU B 366 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN B 457 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ARG B 488 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 460 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AD3, first strand: chain 'B' and resid 545 through 547 Processing sheet with id=AD4, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AD5, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AD6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AD7, first strand: chain 'D' and resid 216 through 217 226 hydrogen bonds defined for protein. 405 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: 7.14 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9593 1.13 - 1.30: 1810 1.30 - 1.48: 4333 1.48 - 1.65: 4755 1.65 - 1.82: 152 Bond restraints: 20643 Sorted by residual: bond pdb=" ND2 ASN B 465 " pdb="HD22 ASN B 465 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL B 83 " pdb=" H VAL B 83 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ILE A 362 " pdb=" H ILE A 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN A 132 " pdb="HE21 GLN A 132 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ PHE B 266 " pdb=" HZ PHE B 266 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 20638 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.56: 255 104.56 - 112.05: 22253 112.05 - 119.54: 6726 119.54 - 127.03: 7507 127.03 - 134.52: 97 Bond angle restraints: 36838 Sorted by residual: angle pdb=" N CYS D 212 " pdb=" CA CYS D 212 " pdb=" C CYS D 212 " ideal model delta sigma weight residual 108.14 115.10 -6.96 1.15e+00 7.56e-01 3.67e+01 angle pdb=" N ILE A 357 " pdb=" CA ILE A 357 " pdb=" C ILE A 357 " ideal model delta sigma weight residual 110.62 116.70 -6.08 1.02e+00 9.61e-01 3.55e+01 angle pdb=" N ALA B 90 " pdb=" CA ALA B 90 " pdb=" C ALA B 90 " ideal model delta sigma weight residual 114.31 121.82 -7.51 1.29e+00 6.01e-01 3.39e+01 angle pdb=" C ARG A 525 " pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " ideal model delta sigma weight residual 117.23 109.58 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" N PHE A 120 " pdb=" CA PHE A 120 " pdb=" C PHE A 120 " ideal model delta sigma weight residual 109.07 117.02 -7.95 1.52e+00 4.33e-01 2.73e+01 ... (remaining 36833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 9881 20.69 - 41.39: 455 41.39 - 62.08: 282 62.08 - 82.77: 88 82.77 - 103.46: 56 Dihedral angle restraints: 10762 sinusoidal: 6378 harmonic: 4384 Sorted by residual: dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -44.44 -41.56 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CB CYS B 217 " pdb=" SG CYS B 217 " pdb=" SG CYS B 229 " pdb=" CB CYS B 229 " ideal model delta sinusoidal sigma weight residual -86.00 -45.35 -40.65 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA LEU B 437 " pdb=" C LEU B 437 " pdb=" N LYS B 438 " pdb=" CA LYS B 438 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 10759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1785 0.309 - 0.618: 16 0.618 - 0.926: 0 0.926 - 1.235: 0 1.235 - 1.544: 1 Chirality restraints: 1802 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.86 -1.54 2.00e-02 2.50e+03 5.96e+03 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.68e+01 ... (remaining 1799 not shown) Planarity restraints: 3125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 495 " 0.299 2.00e-02 2.50e+03 2.38e-01 8.48e+02 pdb=" CG ASN A 495 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 495 " -0.231 2.00e-02 2.50e+03 pdb=" ND2 ASN A 495 " -0.044 2.00e-02 2.50e+03 pdb="HD21 ASN A 495 " -0.309 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " 0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.204 2.00e-02 2.50e+03 1.70e-01 3.61e+02 pdb=" C7 NAG G 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.145 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.280 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 495 " -0.025 2.00e-02 2.50e+03 1.16e-01 1.68e+02 pdb=" CG ASN A 495 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 495 " 0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN A 495 " -0.187 2.00e-02 2.50e+03 pdb="HD21 ASN A 495 " 0.154 2.00e-02 2.50e+03 ... (remaining 3122 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 918 2.10 - 2.73: 29044 2.73 - 3.35: 55365 3.35 - 3.98: 73431 3.98 - 4.60: 106084 Nonbonded interactions: 264842 Sorted by model distance: nonbonded pdb=" O LYS D 187 " pdb=" HG1 THR D 188 " model vdw 1.475 1.850 nonbonded pdb=" OE1 GLN B 164 " pdb=" H GLN B 164 " model vdw 1.598 1.850 nonbonded pdb=" OE1 GLN A 623 " pdb=" H GLN A 623 " model vdw 1.612 1.850 nonbonded pdb=" OE1 GLU B 542 " pdb=" H GLU B 542 " model vdw 1.621 1.850 nonbonded pdb=" OD1 ASP B 349 " pdb=" HG SER B 351 " model vdw 1.621 1.850 ... (remaining 264837 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 26 through 595 or resid 604 through 634 or resid 701)) selection = (chain 'B' and (resid 26 through 634 or resid 701)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'J' selection = chain 'O' } 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: 6.530 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: 0.340 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 66.660 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.014 0.088 11050 Z= 0.869 Angle : 1.559 12.985 14951 Z= 1.021 Chirality : 0.094 1.544 1802 Planarity : 0.010 0.170 1874 Dihedral : 16.961 103.463 4949 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.35 % Allowed : 0.26 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1281 helix: -3.11 (0.39), residues: 96 sheet: -1.20 (0.35), residues: 172 loop : 0.30 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.006 TRP B 407 HIS 0.009 0.001 HIS A 582 PHE 0.063 0.003 PHE D 189 TYR 0.114 0.010 TYR A 157 ARG 0.006 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 LYS cc_start: 0.8573 (pttt) cc_final: 0.8362 (tptp) REVERT: D 217 THR cc_start: 0.8635 (t) cc_final: 0.8422 (p) outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.5823 time to fit residues: 136.3475 Evaluate side-chains 74 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11050 Z= 0.234 Angle : 0.698 7.072 14951 Z= 0.360 Chirality : 0.049 0.268 1802 Planarity : 0.004 0.048 1874 Dihedral : 15.083 82.957 2549 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.21 % Allowed : 4.51 % Favored : 94.28 % 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: -0.72 (0.23), residues: 1281 helix: -2.50 (0.44), residues: 104 sheet: -1.43 (0.34), residues: 182 loop : 0.01 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 407 HIS 0.004 0.001 HIS B 295 PHE 0.010 0.001 PHE A 543 TYR 0.011 0.002 TYR B 148 ARG 0.010 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 TYR cc_start: 0.6446 (p90) cc_final: 0.6002 (p90) REVERT: D 217 THR cc_start: 0.8700 (t) cc_final: 0.8361 (p) outliers start: 14 outliers final: 9 residues processed: 82 average time/residue: 0.5543 time to fit residues: 63.7597 Evaluate side-chains 65 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 30.0000 chunk 127 optimal weight: 0.8980 chunk 105 optimal weight: 0.0030 chunk 117 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11050 Z= 0.162 Angle : 0.583 7.203 14951 Z= 0.293 Chirality : 0.047 0.222 1802 Planarity : 0.004 0.045 1874 Dihedral : 11.417 77.480 2549 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.78 % Allowed : 5.11 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1281 helix: -2.24 (0.45), residues: 104 sheet: -1.48 (0.35), residues: 182 loop : -0.10 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 198 HIS 0.004 0.001 HIS B 295 PHE 0.010 0.001 PHE B 94 TYR 0.007 0.001 TYR A 96 ARG 0.006 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7687 (t0) cc_final: 0.7482 (t0) REVERT: A 526 PHE cc_start: 0.7947 (m-80) cc_final: 0.7674 (m-80) REVERT: B 152 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8133 (m-40) REVERT: B 222 TYR cc_start: 0.6421 (p90) cc_final: 0.6033 (p90) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.5832 time to fit residues: 60.5297 Evaluate side-chains 66 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 30.0000 chunk 88 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11050 Z= 0.222 Angle : 0.574 5.898 14951 Z= 0.293 Chirality : 0.047 0.241 1802 Planarity : 0.004 0.057 1874 Dihedral : 9.342 64.711 2549 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.69 % Allowed : 5.81 % Favored : 93.50 % 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: -0.90 (0.23), residues: 1281 helix: -2.16 (0.46), residues: 105 sheet: -1.49 (0.35), residues: 182 loop : -0.20 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.003 0.001 HIS B 162 PHE 0.011 0.001 PHE B 94 TYR 0.009 0.001 TYR A 123 ARG 0.014 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7765 (t0) cc_final: 0.7530 (t0) REVERT: A 501 MET cc_start: 0.7479 (mmm) cc_final: 0.7262 (mmm) REVERT: B 152 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8130 (m-40) REVERT: B 222 TYR cc_start: 0.6586 (p90) cc_final: 0.6173 (p90) REVERT: B 250 MET cc_start: 0.6723 (pmm) cc_final: 0.6309 (ptp) REVERT: D 219 ASP cc_start: 0.7835 (p0) cc_final: 0.7419 (t0) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.6003 time to fit residues: 56.6909 Evaluate side-chains 63 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN D 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11050 Z= 0.217 Angle : 0.563 6.181 14951 Z= 0.288 Chirality : 0.045 0.218 1802 Planarity : 0.004 0.039 1874 Dihedral : 7.477 57.281 2549 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.30 % Allowed : 5.63 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1281 helix: -2.14 (0.46), residues: 105 sheet: -1.77 (0.35), residues: 174 loop : -0.41 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 198 HIS 0.003 0.001 HIS C 178 PHE 0.016 0.001 PHE B 368 TYR 0.013 0.001 TYR D 224 ARG 0.009 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7743 (t0) cc_final: 0.7517 (t0) REVERT: A 501 MET cc_start: 0.7524 (mmm) cc_final: 0.7298 (mmm) REVERT: B 152 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: B 222 TYR cc_start: 0.6531 (p90) cc_final: 0.6152 (p90) REVERT: B 250 MET cc_start: 0.6682 (pmm) cc_final: 0.6312 (ptp) REVERT: D 219 ASP cc_start: 0.7923 (p0) cc_final: 0.7567 (t0) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.5926 time to fit residues: 59.9490 Evaluate side-chains 65 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11050 Z= 0.262 Angle : 0.560 5.655 14951 Z= 0.290 Chirality : 0.045 0.239 1802 Planarity : 0.004 0.037 1874 Dihedral : 7.155 57.992 2549 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.56 % Allowed : 6.15 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.23), residues: 1281 helix: -2.19 (0.46), residues: 105 sheet: -1.83 (0.36), residues: 174 loop : -0.54 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.004 0.001 HIS B 570 PHE 0.014 0.001 PHE B 368 TYR 0.010 0.001 TYR A 123 ARG 0.007 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7528 (mmm) cc_final: 0.7154 (mmm) REVERT: B 152 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8421 (m-40) REVERT: B 222 TYR cc_start: 0.6501 (p90) cc_final: 0.6194 (p90) REVERT: B 250 MET cc_start: 0.6821 (pmm) cc_final: 0.6477 (ptp) REVERT: D 219 ASP cc_start: 0.7868 (p0) cc_final: 0.7594 (t0) outliers start: 18 outliers final: 12 residues processed: 69 average time/residue: 0.5267 time to fit residues: 52.2543 Evaluate side-chains 64 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11050 Z= 0.215 Angle : 0.539 5.604 14951 Z= 0.280 Chirality : 0.044 0.226 1802 Planarity : 0.004 0.051 1874 Dihedral : 6.711 58.303 2549 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.47 % Allowed : 6.41 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1281 helix: -2.36 (0.44), residues: 105 sheet: -1.79 (0.38), residues: 152 loop : -0.55 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.002 0.001 HIS B 162 PHE 0.012 0.001 PHE B 368 TYR 0.010 0.001 TYR A 468 ARG 0.009 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7435 (mmm) cc_final: 0.7121 (mmm) REVERT: B 152 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8458 (m-40) REVERT: B 222 TYR cc_start: 0.6478 (p90) cc_final: 0.6148 (p90) REVERT: B 250 MET cc_start: 0.6826 (pmm) cc_final: 0.6488 (ptp) REVERT: D 219 ASP cc_start: 0.8018 (p0) cc_final: 0.7683 (t0) outliers start: 17 outliers final: 14 residues processed: 70 average time/residue: 0.5167 time to fit residues: 52.0139 Evaluate side-chains 67 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11050 Z= 0.169 Angle : 0.508 4.922 14951 Z= 0.262 Chirality : 0.043 0.225 1802 Planarity : 0.004 0.044 1874 Dihedral : 6.354 56.755 2549 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.39 % Allowed : 6.85 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1281 helix: -2.30 (0.45), residues: 105 sheet: -1.91 (0.37), residues: 162 loop : -0.53 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 198 HIS 0.002 0.000 HIS B 231 PHE 0.008 0.001 PHE B 368 TYR 0.008 0.001 TYR B 148 ARG 0.006 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7385 (mmm) cc_final: 0.7117 (mmm) REVERT: B 152 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8414 (m-40) REVERT: B 222 TYR cc_start: 0.6494 (p90) cc_final: 0.6141 (p90) REVERT: B 250 MET cc_start: 0.6805 (pmm) cc_final: 0.6466 (ptp) outliers start: 16 outliers final: 12 residues processed: 70 average time/residue: 0.5100 time to fit residues: 51.4038 Evaluate side-chains 63 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 11050 Z= 0.265 Angle : 0.546 5.571 14951 Z= 0.285 Chirality : 0.044 0.234 1802 Planarity : 0.004 0.040 1874 Dihedral : 6.417 56.326 2549 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.56 % Allowed : 7.02 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1281 helix: -2.43 (0.45), residues: 105 sheet: -1.90 (0.37), residues: 164 loop : -0.61 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 198 HIS 0.002 0.001 HIS C 178 PHE 0.014 0.001 PHE B 368 TYR 0.017 0.001 TYR A 469 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7509 (mmm) cc_final: 0.7153 (mmm) REVERT: B 152 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8457 (m-40) REVERT: B 222 TYR cc_start: 0.6459 (p90) cc_final: 0.6073 (p90) REVERT: B 250 MET cc_start: 0.6856 (pmm) cc_final: 0.6502 (ptp) outliers start: 18 outliers final: 16 residues processed: 68 average time/residue: 0.5602 time to fit residues: 53.2883 Evaluate side-chains 68 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain B residue 562 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 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 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 11050 Z= 0.251 Angle : 0.812 59.178 14951 Z= 0.470 Chirality : 0.044 0.232 1802 Planarity : 0.004 0.040 1874 Dihedral : 6.418 56.319 2549 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.30 % Allowed : 7.37 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1281 helix: -2.44 (0.45), residues: 105 sheet: -1.90 (0.37), residues: 164 loop : -0.62 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.002 0.001 HIS C 178 PHE 0.012 0.001 PHE B 368 TYR 0.018 0.001 TYR A 469 ARG 0.003 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7508 (mmm) cc_final: 0.7153 (mmm) REVERT: B 152 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8454 (m-40) REVERT: B 222 TYR cc_start: 0.6458 (p90) cc_final: 0.6067 (p90) REVERT: B 250 MET cc_start: 0.6864 (pmm) cc_final: 0.6511 (ptp) outliers start: 15 outliers final: 14 residues processed: 62 average time/residue: 0.5285 time to fit residues: 47.1352 Evaluate side-chains 64 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain B residue 562 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.154146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097751 restraints weight = 47388.847| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.13 r_work: 0.3298 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 11050 Z= 0.251 Angle : 0.812 59.200 14951 Z= 0.470 Chirality : 0.044 0.232 1802 Planarity : 0.004 0.040 1874 Dihedral : 6.418 56.319 2549 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.30 % Allowed : 7.37 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1281 helix: -2.44 (0.45), residues: 105 sheet: -1.90 (0.37), residues: 164 loop : -0.62 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.002 0.001 HIS C 178 PHE 0.012 0.001 PHE B 368 TYR 0.018 0.001 TYR A 469 ARG 0.003 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4463.42 seconds wall clock time: 78 minutes 43.76 seconds (4723.76 seconds total)