Starting phenix.real_space_refine (version: dev) on Sun Feb 26 09:37:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/02_2023/7cn8_30418_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/02_2023/7cn8_30418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/02_2023/7cn8_30418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/02_2023/7cn8_30418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/02_2023/7cn8_30418_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn8_30418/02_2023/7cn8_30418_neut_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A GLU 1025": "OE1" <-> "OE2" Residue "A ARG 1101": "NH1" <-> "NH2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B GLU 984": "OE1" <-> "OE2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "B ARG 1101": "NH1" <-> "NH2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C GLU 514": "OE1" <-> "OE2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 659": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C GLU 1025": "OE1" <-> "OE2" Residue "C ARG 1101": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27675 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} Chain: "B" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} Chain: "C" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8771 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 54, 'TRANS': 1070} 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 chiralities: 2 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 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 chiralities: 2 Chain: "L" 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 chiralities: 2 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 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 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 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 chiralities: 2 Chain: "T" 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 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 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 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 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 chiralities: 2 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 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 chiralities: 2 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 chiralities: 2 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 chiralities: 2 Chain: "h" 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 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 chiralities: 2 Chain: "k" 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 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 chiralities: 2 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 chiralities: 2 Chain: "H" 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 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 chiralities: 2 Chain: "K" 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 chiralities: 2 Chain: "l" 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 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 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 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 chiralities: 2 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 chiralities: 2 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.96, per 1000 atoms: 0.58 Number of scatterers: 27675 At special positions: 0 Unit cell: (153.715, 141.807, 173.2, 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 123 16.00 O 5475 8.00 N 4491 7.00 C 17586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.06 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.02 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 732 " - pdb=" SG CYS A 754 " distance=2.04 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 834 " - pdb=" SG CYS A 845 " distance=2.03 Simple disulfide: pdb=" SG CYS A1026 " - pdb=" SG CYS A1037 " distance=2.03 Simple disulfide: pdb=" SG CYS A1076 " - pdb=" SG CYS A1120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.07 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.02 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.04 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 754 " distance=2.04 Simple disulfide: pdb=" SG CYS B 737 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 834 " - pdb=" SG CYS B 845 " distance=2.03 Simple disulfide: pdb=" SG CYS B1026 " - pdb=" SG CYS B1037 " distance=2.03 Simple disulfide: pdb=" SG CYS B1076 " - pdb=" SG CYS B1120 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 164 " distance=2.05 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 732 " - pdb=" SG CYS C 754 " distance=2.04 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 834 " - pdb=" SG CYS C 845 " distance=2.03 Simple disulfide: pdb=" SG CYS C1026 " - pdb=" SG CYS C1037 " distance=2.03 Simple disulfide: pdb=" SG CYS C1076 " - pdb=" SG CYS C1120 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " 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 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A1301 " - " ASN A 280 " " NAG A1302 " - " ASN A 341 " " NAG A1303 " - " ASN A 655 " " NAG A1304 " - " ASN A 703 " " NAG A1305 " - " ASN A 601 " " NAG A1306 " - " ASN A 120 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 614 " " NAG A1309 " - " ASN A 329 " " NAG B1301 " - " ASN B 280 " " NAG B1302 " - " ASN B 341 " " NAG B1303 " - " ASN B 655 " " NAG B1304 " - " ASN B 703 " " NAG B1305 " - " ASN B 601 " " NAG B1306 " - " ASN B 120 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 614 " " NAG B1309 " - " ASN B 329 " " NAG C1301 " - " ASN C 280 " " NAG C1302 " - " ASN C 341 " " NAG C1303 " - " ASN C 655 " " NAG C1304 " - " ASN C 703 " " NAG C1305 " - " ASN C 601 " " NAG C1306 " - " ASN C 120 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 614 " " NAG C1309 " - " ASN C 329 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 232 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN A 711 " " NAG H 1 " - " ASN A 795 " " NAG I 1 " - " ASN A1068 " " NAG J 1 " - " ASN A1092 " " NAG K 1 " - " ASN A 163 " " NAG L 1 " - " ASN A 30 " " NAG M 1 " - " ASN A 147 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 795 " " NAG P 1 " - " ASN B 232 " " NAG Q 1 " - " ASN B 368 " " NAG R 1 " - " ASN B1092 " " NAG S 1 " - " ASN B1068 " " NAG T 1 " - " ASN B1128 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN B 163 " " NAG W 1 " - " ASN B 30 " " NAG X 1 " - " ASN B 147 " " NAG Y 1 " - " ASN C 795 " " NAG Z 1 " - " ASN C1068 " " NAG a 1 " - " ASN C 232 " " NAG b 1 " - " ASN C 368 " " NAG e 1 " - " ASN C1128 " " NAG f 1 " - " ASN C1092 " " NAG g 1 " - " ASN C 163 " " NAG h 1 " - " ASN C 30 " " NAG i 1 " - " ASN C 147 " " NAG k 1 " - " ASN A1128 " " NAG l 1 " - " ASN B 711 " " NAG m 1 " - " ASN C 711 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.41 Conformation dependent library (CDL) restraints added in 4.0 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 42 sheets defined 22.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 382 through 387 removed outlier: 4.108A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 437 through 440 No H-bonds generated for 'chain 'A' and resid 437 through 440' Processing helix chain 'A' and resid 615 through 622 Proline residue: A 619 - end of helix removed outlier: 3.533A pdb=" N ILE A 622 " --> pdb=" O PRO A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 629 through 635 removed outlier: 3.559A pdb=" N TYR A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 746 through 776 removed outlier: 3.797A pdb=" N GLN A 749 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 752 " --> pdb=" O GLN A 749 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 766 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 776 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 831 through 836 Processing helix chain 'A' and resid 843 through 849 Processing helix chain 'A' and resid 861 through 882 removed outlier: 7.657A pdb=" N TRP A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 881 " --> pdb=" O THR A 877 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A 882 " --> pdb=" O SER A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 902 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 914 through 934 Processing helix chain 'A' and resid 940 through 961 removed outlier: 3.579A pdb=" N LEU A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 977 Processing helix chain 'A' and resid 980 through 1026 removed outlier: 3.795A pdb=" N VAL A 985 " --> pdb=" O PRO A 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1122 No H-bonds generated for 'chain 'A' and resid 1120 through 1122' Processing helix chain 'A' and resid 1134 through 1137 No H-bonds generated for 'chain 'A' and resid 1134 through 1137' Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 382 through 387 removed outlier: 4.109A pdb=" N ASN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 437 through 440 No H-bonds generated for 'chain 'B' and resid 437 through 440' Processing helix chain 'B' and resid 615 through 622 Proline residue: B 619 - end of helix removed outlier: 3.533A pdb=" N ILE B 622 " --> pdb=" O PRO B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 626 No H-bonds generated for 'chain 'B' and resid 624 through 626' Processing helix chain 'B' and resid 629 through 635 removed outlier: 3.559A pdb=" N TYR B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 746 through 776 removed outlier: 3.797A pdb=" N GLN B 749 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 752 " --> pdb=" O GLN B 749 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 766 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 776 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 819 Processing helix chain 'B' and resid 831 through 836 Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 861 through 882 removed outlier: 7.657A pdb=" N TRP B 880 " --> pdb=" O ILE B 876 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR B 881 " --> pdb=" O THR B 877 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B 882 " --> pdb=" O SER B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 902 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 914 through 934 Processing helix chain 'B' and resid 940 through 961 removed outlier: 3.579A pdb=" N LEU B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 961 " --> pdb=" O VAL B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 977 Processing helix chain 'B' and resid 980 through 1026 removed outlier: 3.795A pdb=" N VAL B 985 " --> pdb=" O PRO B 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 986 " --> pdb=" O GLU B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1134 through 1137 No H-bonds generated for 'chain 'B' and resid 1134 through 1137' Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 382 through 387 removed outlier: 4.108A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 437 through 440 No H-bonds generated for 'chain 'C' and resid 437 through 440' Processing helix chain 'C' and resid 615 through 622 Proline residue: C 619 - end of helix removed outlier: 3.533A pdb=" N ILE C 622 " --> pdb=" O PRO C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 626 No H-bonds generated for 'chain 'C' and resid 624 through 626' Processing helix chain 'C' and resid 629 through 635 removed outlier: 3.559A pdb=" N TYR C 634 " --> pdb=" O ALA C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 737 Processing helix chain 'C' and resid 746 through 776 removed outlier: 3.797A pdb=" N GLN C 749 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 752 " --> pdb=" O GLN C 749 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 766 " --> pdb=" O GLY C 763 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 776 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 819 Processing helix chain 'C' and resid 831 through 836 Processing helix chain 'C' and resid 843 through 849 Processing helix chain 'C' and resid 861 through 882 removed outlier: 7.657A pdb=" N TRP C 880 " --> pdb=" O ILE C 876 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR C 881 " --> pdb=" O THR C 877 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE C 882 " --> pdb=" O SER C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 902 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 914 through 934 Processing helix chain 'C' and resid 940 through 961 removed outlier: 3.579A pdb=" N LEU C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER C 961 " --> pdb=" O VAL C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 977 Processing helix chain 'C' and resid 980 through 1026 removed outlier: 3.795A pdb=" N VAL C 985 " --> pdb=" O PRO C 981 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 986 " --> pdb=" O GLU C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1122 No H-bonds generated for 'chain 'C' and resid 1120 through 1122' Processing helix chain 'C' and resid 1134 through 1137 No H-bonds generated for 'chain 'C' and resid 1134 through 1137' Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.165A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 225 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP A 285 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.678A pdb=" N GLY A 101 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 138 through 142 removed outlier: 6.515A pdb=" N LEU A 240 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A 141 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 242 " --> pdb=" O VAL A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 322 through 326 removed outlier: 4.813A pdb=" N ILE A 322 " --> pdb=" O CYS A 536 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL A 393 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 359 through 361 Processing sheet with id= H, first strand: chain 'A' and resid 450 through 452 Processing sheet with id= I, first strand: chain 'A' and resid 594 through 597 Processing sheet with id= J, first strand: chain 'A' and resid 685 through 690 removed outlier: 6.512A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA A1072 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A1089 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 712 through 722 removed outlier: 5.895A pdb=" N TYR A1061 " --> pdb=" O HIS A1042 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS A1042 " --> pdb=" O TYR A1061 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 727 through 730 removed outlier: 4.306A pdb=" N LYS A 727 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1082 through 1084 Processing sheet with id= O, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.165A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 225 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP B 285 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.677A pdb=" N GLY B 101 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 139 through 142 Processing sheet with id= S, first strand: chain 'B' and resid 322 through 326 removed outlier: 4.813A pdb=" N ILE B 322 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL B 393 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 359 through 361 Processing sheet with id= V, first strand: chain 'B' and resid 450 through 452 Processing sheet with id= W, first strand: chain 'B' and resid 594 through 597 Processing sheet with id= X, first strand: chain 'B' and resid 685 through 690 removed outlier: 6.512A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA B1072 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B1089 " --> pdb=" O ALA B1072 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 712 through 722 removed outlier: 5.895A pdb=" N TYR B1061 " --> pdb=" O HIS B1042 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS B1042 " --> pdb=" O TYR B1061 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 727 through 730 removed outlier: 4.305A pdb=" N LYS B 727 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 1082 through 1084 Processing sheet with id= AC, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.166A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.948A pdb=" N ASP C 285 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.677A pdb=" N GLY C 101 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.510A pdb=" N LEU C 240 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL C 141 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 242 " --> pdb=" O VAL C 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'C' and resid 322 through 326 removed outlier: 4.812A pdb=" N ILE C 322 " --> pdb=" O CYS C 536 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.337A pdb=" N VAL C 393 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 359 through 361 Processing sheet with id= AJ, first strand: chain 'C' and resid 450 through 452 Processing sheet with id= AK, first strand: chain 'C' and resid 594 through 597 Processing sheet with id= AL, first strand: chain 'C' and resid 685 through 690 removed outlier: 6.513A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 705 through 709 removed outlier: 3.699A pdb=" N ALA C1072 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C1089 " --> pdb=" O ALA C1072 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 712 through 722 removed outlier: 5.896A pdb=" N TYR C1061 " --> pdb=" O HIS C1042 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS C1042 " --> pdb=" O TYR C1061 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 727 through 730 removed outlier: 4.306A pdb=" N LYS C 727 " --> pdb=" O LEU C 855 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 1082 through 1084 927 hydrogen bonds defined for protein. 2376 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: 11.95 Time building geometry restraints manager: 13.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5398 1.33 - 1.45: 7102 1.45 - 1.57: 15628 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28284 Sorted by residual: bond pdb=" C12 EIC B1310 " pdb=" C13 EIC B1310 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C12 EIC A1310 " pdb=" C13 EIC A1310 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.56e+01 bond pdb=" C10 EIC A1310 " pdb=" C9 EIC A1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C12 EIC C1310 " pdb=" C13 EIC C1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C10 EIC C1310 " pdb=" C9 EIC C1310 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.51e+01 ... (remaining 28279 not shown) Histogram of bond angle deviations from ideal: 100.18 - 107.07: 914 107.07 - 113.96: 15900 113.96 - 120.85: 13523 120.85 - 127.74: 8040 127.74 - 134.63: 116 Bond angle restraints: 38493 Sorted by residual: angle pdb=" C THR B 248 " pdb=" CA THR B 248 " pdb=" CB THR B 248 " ideal model delta sigma weight residual 111.20 117.42 -6.22 7.10e-01 1.98e+00 7.67e+01 angle pdb=" C THR A 248 " pdb=" CA THR A 248 " pdb=" CB THR A 248 " ideal model delta sigma weight residual 111.20 117.42 -6.22 7.10e-01 1.98e+00 7.67e+01 angle pdb=" C THR C 248 " pdb=" CA THR C 248 " pdb=" CB THR C 248 " ideal model delta sigma weight residual 111.20 117.40 -6.20 7.10e-01 1.98e+00 7.62e+01 angle pdb=" N PRO C 980 " pdb=" CA PRO C 980 " pdb=" C PRO C 980 " ideal model delta sigma weight residual 110.70 119.56 -8.86 1.22e+00 6.72e-01 5.27e+01 angle pdb=" N PRO B 980 " pdb=" CA PRO B 980 " pdb=" C PRO B 980 " ideal model delta sigma weight residual 110.70 119.53 -8.83 1.22e+00 6.72e-01 5.23e+01 ... (remaining 38488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 15584 21.85 - 43.70: 886 43.70 - 65.55: 146 65.55 - 87.40: 40 87.40 - 109.25: 3 Dihedral angle restraints: 16659 sinusoidal: 6849 harmonic: 9810 Sorted by residual: dihedral pdb=" C CYS C 164 " pdb=" N CYS C 164 " pdb=" CA CYS C 164 " pdb=" CB CYS C 164 " ideal model delta harmonic sigma weight residual -122.60 -140.88 18.28 0 2.50e+00 1.60e-01 5.35e+01 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 152.38 -59.38 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" N CYS C 164 " pdb=" C CYS C 164 " pdb=" CA CYS C 164 " pdb=" CB CYS C 164 " ideal model delta harmonic sigma weight residual 122.80 139.00 -16.20 0 2.50e+00 1.60e-01 4.20e+01 ... (remaining 16656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3968 0.164 - 0.329: 639 0.329 - 0.493: 24 0.493 - 0.657: 0 0.657 - 0.822: 4 Chirality restraints: 4635 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 -1.94 -0.46 2.00e-02 2.50e+03 5.33e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+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 -2.19 -0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 4632 not shown) Planarity restraints: 4920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG O 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIC A1310 " 0.420 2.00e-02 2.50e+03 3.16e-01 1.00e+03 pdb=" C11 EIC A1310 " -0.155 2.00e-02 2.50e+03 pdb=" C8 EIC A1310 " 0.155 2.00e-02 2.50e+03 pdb=" C9 EIC A1310 " -0.419 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.323 2.00e-02 2.50e+03 2.81e-01 9.86e+02 pdb=" C7 NAG A1301 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.126 2.00e-02 2.50e+03 ... (remaining 4917 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 118 2.63 - 3.20: 23345 3.20 - 3.76: 42381 3.76 - 4.33: 61539 4.33 - 4.90: 97379 Nonbonded interactions: 224762 Sorted by model distance: nonbonded pdb=" O3 NAG Y 2 " pdb=" O7 NAG Y 2 " model vdw 2.059 2.440 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.073 2.440 nonbonded pdb=" OG1 THR B 22 " pdb=" O LYS B 75 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR C 22 " pdb=" O LYS C 75 " model vdw 2.266 2.440 nonbonded pdb=" CG2 ILE A 838 " pdb=" OD2 ASP C 584 " model vdw 2.282 3.460 ... (remaining 224757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 17586 2.51 5 N 4491 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.870 Check model and map are aligned: 0.460 Process input model: 73.780 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.013 0.196 28284 Z= 0.868 Angle : 1.557 15.164 38493 Z= 1.187 Chirality : 0.113 0.822 4635 Planarity : 0.022 0.316 4860 Dihedral : 13.841 109.251 10236 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.53 % Favored : 96.05 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.70 % 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: 1.41 (0.14), residues: 3369 helix: 4.20 (0.19), residues: 690 sheet: 1.75 (0.19), residues: 609 loop : -0.52 (0.12), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 272 time to evaluate : 3.345 Fit side-chains revert: symmetry clash outliers start: 143 outliers final: 22 residues processed: 397 average time/residue: 1.0559 time to fit residues: 512.8176 Evaluate side-chains 143 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.2349 time to fit residues: 4.4501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 305 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 85 ASN A 113 GLN A 119 ASN A 472 GLN A 496 HIS A 758 ASN A 895 GLN A1113 ASN B 71 GLN B 85 ASN B 119 ASN B 496 HIS B 626 GLN B 697 ASN B 758 ASN B 895 GLN C 71 GLN C 85 ASN C 113 GLN C 119 ASN C 472 GLN C 496 HIS C 697 ASN C 758 ASN C 895 GLN C1113 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 28284 Z= 0.206 Angle : 0.595 6.970 38493 Z= 0.344 Chirality : 0.049 0.566 4635 Planarity : 0.004 0.034 4860 Dihedral : 8.125 108.731 4242 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer Outliers : 2.97 % 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: 0.65 (0.14), residues: 3369 helix: 2.46 (0.19), residues: 735 sheet: 1.23 (0.18), residues: 735 loop : -0.76 (0.13), residues: 1899 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 142 time to evaluate : 3.201 Fit side-chains outliers start: 87 outliers final: 36 residues processed: 216 average time/residue: 0.9373 time to fit residues: 256.3227 Evaluate side-chains 142 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 3.327 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 35 residues processed: 1 average time/residue: 0.2748 time to fit residues: 4.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.1980 chunk 94 optimal weight: 0.2980 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 chunk 272 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN B 144 HIS B 153 ASN C 153 ASN C 562 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 28284 Z= 0.238 Angle : 0.569 12.037 38493 Z= 0.318 Chirality : 0.047 0.574 4635 Planarity : 0.004 0.043 4860 Dihedral : 8.264 110.431 4242 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer Outliers : 3.14 % 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 (0.14), residues: 3369 helix: 1.71 (0.19), residues: 735 sheet: 1.08 (0.19), residues: 726 loop : -0.94 (0.13), residues: 1908 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 125 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 37 residues processed: 203 average time/residue: 0.9402 time to fit residues: 242.9571 Evaluate side-chains 148 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 111 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 4 average time/residue: 0.5017 time to fit residues: 6.9244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 290 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 97 ASN B 119 ASN B 153 ASN B 830 GLN C 153 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 28284 Z= 0.209 Angle : 0.523 7.572 38493 Z= 0.293 Chirality : 0.046 0.512 4635 Planarity : 0.004 0.045 4860 Dihedral : 8.162 110.439 4242 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 2.77 % 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: 0.01 (0.14), residues: 3369 helix: 1.43 (0.19), residues: 753 sheet: 1.03 (0.19), residues: 696 loop : -1.02 (0.13), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 122 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 41 residues processed: 193 average time/residue: 1.0584 time to fit residues: 255.5650 Evaluate side-chains 145 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 3.242 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 3 average time/residue: 0.2477 time to fit residues: 5.8406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.0980 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 270 GLN C 153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28284 Z= 0.219 Angle : 0.525 8.187 38493 Z= 0.293 Chirality : 0.046 0.500 4635 Planarity : 0.004 0.046 4860 Dihedral : 8.106 110.763 4242 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 3.18 % 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: -0.15 (0.14), residues: 3369 helix: 1.09 (0.19), residues: 789 sheet: 0.92 (0.19), residues: 705 loop : -1.07 (0.13), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 122 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 40 residues processed: 199 average time/residue: 1.0456 time to fit residues: 258.7773 Evaluate side-chains 152 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 112 time to evaluate : 3.465 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 35 residues processed: 5 average time/residue: 0.4615 time to fit residues: 7.9877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN A 697 ASN B 153 ASN B 270 GLN C 153 ASN C 562 GLN C 895 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 28284 Z= 0.259 Angle : 0.547 10.701 38493 Z= 0.304 Chirality : 0.046 0.496 4635 Planarity : 0.004 0.050 4860 Dihedral : 8.105 110.960 4242 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 2.56 % 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 (0.14), residues: 3369 helix: 1.10 (0.19), residues: 771 sheet: 0.68 (0.19), residues: 738 loop : -1.09 (0.13), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 123 time to evaluate : 3.510 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 42 residues processed: 192 average time/residue: 1.0771 time to fit residues: 257.8181 Evaluate side-chains 149 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 107 time to evaluate : 3.542 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 39 residues processed: 3 average time/residue: 0.6809 time to fit residues: 7.7595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 119 ASN B 52 GLN B 270 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 28284 Z= 0.224 Angle : 0.538 10.642 38493 Z= 0.298 Chirality : 0.045 0.488 4635 Planarity : 0.004 0.049 4860 Dihedral : 8.076 111.244 4242 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 2.32 % 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: -0.29 (0.14), residues: 3369 helix: 1.12 (0.19), residues: 765 sheet: 0.63 (0.19), residues: 735 loop : -1.14 (0.13), residues: 1869 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 121 time to evaluate : 3.302 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 40 residues processed: 182 average time/residue: 1.0463 time to fit residues: 245.3294 Evaluate side-chains 149 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 0.3652 time to fit residues: 5.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN B 97 ASN B 626 GLN C 270 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 28284 Z= 0.382 Angle : 0.614 10.753 38493 Z= 0.340 Chirality : 0.049 0.510 4635 Planarity : 0.005 0.050 4860 Dihedral : 8.375 110.458 4242 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.03 % 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: -0.56 (0.14), residues: 3369 helix: 0.92 (0.19), residues: 765 sheet: 0.31 (0.19), residues: 729 loop : -1.23 (0.13), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 117 time to evaluate : 3.671 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 45 residues processed: 175 average time/residue: 1.1432 time to fit residues: 248.0799 Evaluate side-chains 158 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 113 time to evaluate : 3.361 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 41 residues processed: 4 average time/residue: 0.5451 time to fit residues: 7.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 283 optimal weight: 0.6980 chunk 301 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 272 optimal weight: 3.9990 chunk 285 optimal weight: 0.3980 chunk 300 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN A 895 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN C 270 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 GLN C 951 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 28284 Z= 0.185 Angle : 0.530 10.921 38493 Z= 0.293 Chirality : 0.045 0.476 4635 Planarity : 0.004 0.048 4860 Dihedral : 8.115 110.967 4242 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.41 (0.14), residues: 3369 helix: 1.05 (0.19), residues: 762 sheet: 0.58 (0.18), residues: 777 loop : -1.27 (0.13), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 116 time to evaluate : 3.316 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 36 residues processed: 171 average time/residue: 1.1048 time to fit residues: 235.7140 Evaluate side-chains 143 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 36 residues processed: 0 time to fit residues: 4.5951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 266 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN B 929 GLN C 798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 28284 Z= 0.160 Angle : 0.506 10.688 38493 Z= 0.277 Chirality : 0.044 0.464 4635 Planarity : 0.004 0.048 4860 Dihedral : 7.908 111.030 4242 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.37 (0.14), residues: 3369 helix: 1.13 (0.19), residues: 762 sheet: 0.50 (0.19), residues: 741 loop : -1.19 (0.13), residues: 1866 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 3.097 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 36 residues processed: 155 average time/residue: 1.2431 time to fit residues: 242.4416 Evaluate side-chains 139 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 35 residues processed: 1 average time/residue: 0.4911 time to fit residues: 5.0579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 274 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 929 GLN C 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077349 restraints weight = 47418.754| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.73 r_work: 0.2987 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 28284 Z= 0.198 Angle : 0.522 10.962 38493 Z= 0.287 Chirality : 0.044 0.469 4635 Planarity : 0.004 0.048 4860 Dihedral : 7.960 110.788 4242 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3369 helix: 1.12 (0.19), residues: 762 sheet: 0.47 (0.19), residues: 741 loop : -1.21 (0.13), residues: 1866 =============================================================================== Job complete usr+sys time: 7153.99 seconds wall clock time: 130 minutes 44.52 seconds (7844.52 seconds total)