Starting phenix.real_space_refine on Sat Mar 16 20:28:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8b_23228/03_2024/7l8b_23228_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8b_23228/03_2024/7l8b_23228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8b_23228/03_2024/7l8b_23228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8b_23228/03_2024/7l8b_23228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8b_23228/03_2024/7l8b_23228_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8b_23228/03_2024/7l8b_23228_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9776 2.51 5 N 2634 2.21 5 O 3195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15704 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3463 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3424 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "L" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.76, per 1000 atoms: 0.56 Number of scatterers: 15704 At special positions: 0 Unit cell: (141.11, 125.66, 120.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3195 8.00 N 2634 7.00 C 9776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.06 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.02 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA U 3 " - " MAN U 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA U 3 " - " MAN U 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 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 U 2 " - " BMA U 3 " " 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " 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-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 448 " " NAG A 605 " - " ASN A 137 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 88 " " NAG C 608 " - " ASN C 137 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 137 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN C 156 " " NAG I 1 " - " ASN C 197 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN C 448 " " NAG Q 1 " - " ASN A 133 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 276 " " NAG W 1 " - " ASN A 295 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 386 " " NAG Z 1 " - " ASN A 392 " " NAG a 1 " - " ASN A 88 " " NAG b 1 " - " ASN E 156 " " NAG c 1 " - " ASN E 197 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 276 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 332 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 448 " Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 2.6 seconds 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 33 sheets defined 25.7% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.131A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.568A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 543 removed outlier: 3.890A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 542 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 663 removed outlier: 4.738A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.344A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.001A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.141A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.533A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 663 removed outlier: 5.196A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 643 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 removed outlier: 4.173A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 475 through 482 removed outlier: 3.603A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 536 removed outlier: 4.371A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 663 removed outlier: 5.026A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 642 " --> pdb=" O THR F 639 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'L' and resid 31 through 33 No H-bonds generated for 'chain 'L' and resid 31 through 33' Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.734A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= D, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= E, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= F, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.597A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.910A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 301 through 308 removed outlier: 4.322A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= J, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.900A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.559A pdb=" N HIS A 216 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= M, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= N, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.787A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.694A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 443 through 449 removed outlier: 3.906A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.526A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 301 through 308 removed outlier: 4.055A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= U, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.896A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= X, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= Y, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= Z, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.447A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.905A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 301 through 307 removed outlier: 3.956A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AD, first strand: chain 'H' and resid 115 through 117 removed outlier: 6.104A pdb=" N UNK H 40 " --> pdb=" O UNK H 49 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N UNK H 49 " --> pdb=" O UNK H 40 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'L' and resid 9 through 11 removed outlier: 8.784A pdb=" N UNK L 10 " --> pdb=" O UNK L 105 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N UNK L 107 " --> pdb=" O UNK L 10 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK L 104 " --> pdb=" O UNK L 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N UNK L 93 " --> pdb=" O UNK L 104 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK L 37 " --> pdb=" O UNK L 94 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N UNK L 40 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N UNK L 49 " --> pdb=" O UNK L 40 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 99 through 101 removed outlier: 3.515A pdb=" N UNK H 110 " --> pdb=" O UNK H 100 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1257 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: 4.82 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3634 1.32 - 1.46: 4954 1.46 - 1.60: 7236 1.60 - 1.74: 23 1.74 - 1.87: 126 Bond restraints: 15973 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.408 -0.082 1.10e-02 8.26e+03 5.51e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.39e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.395 -0.069 1.10e-02 8.26e+03 3.95e+01 bond pdb=" CG GLN B 540 " pdb=" CD GLN B 540 " ideal model delta sigma weight residual 1.516 1.361 0.155 2.50e-02 1.60e+03 3.83e+01 bond pdb=" CB ILE E 396 " pdb=" CG1 ILE E 396 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 15968 not shown) Histogram of bond angle deviations from ideal: 94.02 - 102.06: 56 102.06 - 110.09: 4818 110.09 - 118.13: 8170 118.13 - 126.17: 8365 126.17 - 134.20: 323 Bond angle restraints: 21732 Sorted by residual: angle pdb=" N GLY C 471 " pdb=" CA GLY C 471 " pdb=" C GLY C 471 " ideal model delta sigma weight residual 110.38 94.02 16.36 1.48e+00 4.57e-01 1.22e+02 angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 112.43 120.46 -8.03 9.20e-01 1.18e+00 7.62e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 128.03 -8.47 1.02e+00 9.61e-01 6.89e+01 angle pdb=" N SER A 56 " pdb=" CA SER A 56 " pdb=" C SER A 56 " ideal model delta sigma weight residual 111.28 120.18 -8.90 1.09e+00 8.42e-01 6.67e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 127.32 -7.76 1.02e+00 9.61e-01 5.78e+01 ... (remaining 21727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 10482 21.23 - 42.46: 230 42.46 - 63.70: 77 63.70 - 84.93: 28 84.93 - 106.16: 14 Dihedral angle restraints: 10831 sinusoidal: 5296 harmonic: 5535 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.71 -60.71 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" N ASP A 57 " pdb=" C ASP A 57 " pdb=" CA ASP A 57 " pdb=" CB ASP A 57 " ideal model delta harmonic sigma weight residual 122.80 140.18 -17.38 0 2.50e+00 1.60e-01 4.83e+01 dihedral pdb=" C ASP A 57 " pdb=" N ASP A 57 " pdb=" CA ASP A 57 " pdb=" CB ASP A 57 " ideal model delta harmonic sigma weight residual -122.60 -139.90 17.30 0 2.50e+00 1.60e-01 4.79e+01 ... (remaining 10828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 2400 0.217 - 0.435: 343 0.435 - 0.652: 36 0.652 - 0.870: 1 0.870 - 1.087: 1 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.83e+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 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 2778 not shown) Planarity restraints: 2719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG Z 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.357 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG I 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 703 " -0.330 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG D 703 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG D 703 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG D 703 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG D 703 " -0.201 2.00e-02 2.50e+03 ... (remaining 2716 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.95: 2 1.95 - 2.69: 862 2.69 - 3.43: 20224 3.43 - 4.16: 37228 4.16 - 4.90: 61539 Nonbonded interactions: 119855 Sorted by model distance: nonbonded pdb=" OG SER E 393 " pdb=" CZ3 TRP E 395 " model vdw 1.218 3.340 nonbonded pdb=" OG SER E 393 " pdb=" CH2 TRP E 395 " model vdw 1.814 3.340 nonbonded pdb=" O3 NAG I 1 " pdb=" O7 NAG I 1 " model vdw 2.052 2.440 nonbonded pdb=" CB SER E 393 " pdb=" CZ3 TRP E 395 " model vdw 2.170 3.740 nonbonded pdb=" O ILE C 453 " pdb=" O GLY C 471 " model vdw 2.301 3.040 ... (remaining 119850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 458 or resid 463 through \ 503 or resid 601 through 605)) selection = (chain 'C' and (resid 33 through 397 or resid 411 through 503 or resid 601 throu \ gh 605)) selection = (chain 'E' and (resid 33 through 503 or resid 601 through 605)) } ncs_group { reference = (chain 'B' and (resid 519 through 664 or resid 701 through 703)) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' 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 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = (chain 'H' and resid 12 through 119) selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'U' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.020 Extract box with map and model: 10.770 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 44.730 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.155 15973 Z= 1.408 Angle : 1.719 16.358 21732 Z= 1.099 Chirality : 0.149 1.087 2781 Planarity : 0.015 0.306 2662 Dihedral : 11.185 106.162 7128 Min Nonbonded Distance : 1.218 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.11 % 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: 1.11 (0.19), residues: 1642 helix: 0.71 (0.24), residues: 396 sheet: 1.35 (0.24), residues: 384 loop : 0.61 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.008 TRP A 96 HIS 0.008 0.002 HIS A 216 PHE 0.029 0.006 PHE A 383 TYR 0.047 0.007 TYR B 638 ARG 0.007 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 THR cc_start: 0.9412 (m) cc_final: 0.9132 (p) REVERT: D 602 LEU cc_start: 0.9090 (mt) cc_final: 0.8804 (mt) REVERT: D 603 ILE cc_start: 0.9380 (mt) cc_final: 0.9174 (mp) REVERT: D 616 ASN cc_start: 0.8682 (p0) cc_final: 0.8446 (p0) REVERT: D 653 GLN cc_start: 0.8226 (tt0) cc_final: 0.7977 (tm-30) REVERT: A 75 VAL cc_start: 0.8617 (t) cc_final: 0.8139 (m) REVERT: B 590 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8939 (mm-40) REVERT: E 248 THR cc_start: 0.9502 (p) cc_final: 0.9255 (p) REVERT: F 536 THR cc_start: 0.9582 (p) cc_final: 0.9367 (p) REVERT: F 543 ASN cc_start: 0.8439 (m-40) cc_final: 0.8095 (m110) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2953 time to fit residues: 178.7423 Evaluate side-chains 196 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 130 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 185 ASN A 203 GLN B 577 GLN E 33 ASN E 130 GLN E 302 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15973 Z= 0.232 Angle : 0.707 15.502 21732 Z= 0.361 Chirality : 0.048 0.316 2781 Planarity : 0.005 0.034 2662 Dihedral : 8.564 84.005 3956 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.94 % Allowed : 8.88 % Favored : 89.18 % 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: 0.79 (0.20), residues: 1642 helix: 0.96 (0.25), residues: 393 sheet: 0.85 (0.24), residues: 425 loop : 0.26 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 571 HIS 0.005 0.001 HIS A 249 PHE 0.017 0.003 PHE C 159 TYR 0.022 0.002 TYR A 435 ARG 0.005 0.001 ARG C 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 257 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8984 (m-80) cc_final: 0.8760 (m-10) REVERT: C 202 THR cc_start: 0.9308 (m) cc_final: 0.9073 (p) REVERT: A 75 VAL cc_start: 0.8687 (t) cc_final: 0.8480 (m) REVERT: A 289 ASN cc_start: 0.8473 (p0) cc_final: 0.8208 (p0) REVERT: A 381 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6940 (mm-30) REVERT: E 46 LYS cc_start: 0.8357 (mtmt) cc_final: 0.7237 (mtmt) REVERT: E 368 ASP cc_start: 0.6624 (p0) cc_final: 0.6421 (p0) REVERT: F 543 ASN cc_start: 0.8439 (m-40) cc_final: 0.8045 (m110) REVERT: F 617 ARG cc_start: 0.8370 (mtt180) cc_final: 0.8130 (mtt180) outliers start: 29 outliers final: 14 residues processed: 281 average time/residue: 0.2423 time to fit residues: 103.6107 Evaluate side-chains 210 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN D 591 GLN D 652 GLN A 203 GLN B 577 GLN B 625 ASN B 640 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 377 ASN E 411 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 15973 Z= 0.501 Angle : 0.832 12.227 21732 Z= 0.418 Chirality : 0.051 0.265 2781 Planarity : 0.006 0.066 2662 Dihedral : 8.631 74.354 3956 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.21 % Allowed : 10.49 % Favored : 85.30 % 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: -0.06 (0.20), residues: 1642 helix: 0.11 (0.25), residues: 391 sheet: 0.61 (0.25), residues: 410 loop : -0.37 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 45 HIS 0.009 0.002 HIS E 105 PHE 0.025 0.003 PHE A 176 TYR 0.021 0.003 TYR C 435 ARG 0.008 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 197 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 640 GLN cc_start: 0.8349 (tp40) cc_final: 0.7889 (tp40) REVERT: A 75 VAL cc_start: 0.8737 (t) cc_final: 0.8497 (m) REVERT: A 90 THR cc_start: 0.9338 (m) cc_final: 0.9111 (p) REVERT: A 161 MET cc_start: 0.8474 (tpt) cc_final: 0.8155 (tpt) REVERT: F 617 ARG cc_start: 0.8321 (mtt180) cc_final: 0.7705 (mtt180) outliers start: 63 outliers final: 45 residues processed: 242 average time/residue: 0.2672 time to fit residues: 97.4491 Evaluate side-chains 209 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 114 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN B 577 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15973 Z= 0.172 Angle : 0.576 9.648 21732 Z= 0.293 Chirality : 0.045 0.346 2781 Planarity : 0.004 0.054 2662 Dihedral : 7.340 67.585 3956 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.87 % Allowed : 13.76 % Favored : 84.37 % 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: 0.09 (0.20), residues: 1642 helix: 0.33 (0.26), residues: 399 sheet: 0.77 (0.25), residues: 398 loop : -0.34 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.003 0.001 HIS E 105 PHE 0.014 0.002 PHE C 159 TYR 0.015 0.001 TYR A 191 ARG 0.004 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9185 (m-80) cc_final: 0.8951 (m-10) REVERT: C 202 THR cc_start: 0.9351 (m) cc_final: 0.8928 (p) REVERT: D 640 GLN cc_start: 0.8221 (tp40) cc_final: 0.8001 (tp40) REVERT: A 75 VAL cc_start: 0.8704 (t) cc_final: 0.8503 (m) REVERT: A 161 MET cc_start: 0.8584 (tpt) cc_final: 0.7996 (tpt) REVERT: A 217 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: A 289 ASN cc_start: 0.8512 (p0) cc_final: 0.8279 (p0) REVERT: B 655 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8770 (mtpt) REVERT: E 46 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8058 (mtmt) REVERT: E 151 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7867 (ptt90) REVERT: E 194 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8964 (tp) REVERT: E 492 GLU cc_start: 0.8096 (tt0) cc_final: 0.7689 (mt-10) outliers start: 28 outliers final: 17 residues processed: 223 average time/residue: 0.2682 time to fit residues: 89.2977 Evaluate side-chains 199 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 654 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 154 optimal weight: 0.0770 chunk 124 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 0.0020 chunk 162 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15973 Z= 0.250 Angle : 0.587 9.622 21732 Z= 0.296 Chirality : 0.045 0.273 2781 Planarity : 0.004 0.057 2662 Dihedral : 7.009 63.803 3956 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.01 % Allowed : 13.43 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1642 helix: 0.41 (0.26), residues: 392 sheet: 0.66 (0.24), residues: 424 loop : -0.34 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.004 0.001 HIS E 105 PHE 0.011 0.002 PHE A 383 TYR 0.011 0.001 TYR A 191 ARG 0.004 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 640 GLN cc_start: 0.8251 (tp40) cc_final: 0.7933 (tp40) REVERT: A 75 VAL cc_start: 0.8726 (t) cc_final: 0.8521 (m) REVERT: A 217 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: B 586 TYR cc_start: 0.9255 (t80) cc_final: 0.9049 (t80) REVERT: B 655 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8793 (mtpt) REVERT: E 151 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7858 (ptt90) REVERT: E 194 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8961 (tp) REVERT: F 625 ASN cc_start: 0.8453 (m110) cc_final: 0.8236 (m-40) outliers start: 45 outliers final: 33 residues processed: 217 average time/residue: 0.2760 time to fit residues: 90.1426 Evaluate side-chains 211 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15973 Z= 0.403 Angle : 0.689 8.601 21732 Z= 0.344 Chirality : 0.048 0.274 2781 Planarity : 0.005 0.064 2662 Dihedral : 7.492 61.376 3956 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.34 % Allowed : 12.89 % Favored : 82.77 % 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: -0.33 (0.20), residues: 1642 helix: 0.10 (0.25), residues: 392 sheet: 0.40 (0.25), residues: 406 loop : -0.62 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 35 HIS 0.006 0.001 HIS C 330 PHE 0.016 0.002 PHE A 176 TYR 0.015 0.002 TYR E 217 ARG 0.005 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 182 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.8928 (m) REVERT: C 202 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.8911 (p) REVERT: D 640 GLN cc_start: 0.8401 (tp40) cc_final: 0.8096 (tp40) REVERT: A 75 VAL cc_start: 0.8772 (t) cc_final: 0.8520 (m) REVERT: A 217 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: A 432 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: B 586 TYR cc_start: 0.9332 (t80) cc_final: 0.9131 (t80) REVERT: B 655 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8762 (mtpt) REVERT: E 151 ARG cc_start: 0.8174 (ptm160) cc_final: 0.7785 (ptt90) REVERT: E 194 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9026 (tp) outliers start: 65 outliers final: 46 residues processed: 226 average time/residue: 0.2782 time to fit residues: 93.0342 Evaluate side-chains 225 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 174 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 132 optimal weight: 0.0770 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN D 575 GLN A 66 HIS B 577 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15973 Z= 0.156 Angle : 0.546 8.220 21732 Z= 0.276 Chirality : 0.044 0.267 2781 Planarity : 0.004 0.055 2662 Dihedral : 6.542 56.795 3956 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.47 % Allowed : 15.03 % Favored : 82.50 % 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: -0.10 (0.20), residues: 1642 helix: 0.33 (0.26), residues: 398 sheet: 0.69 (0.24), residues: 417 loop : -0.62 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 35 HIS 0.004 0.000 HIS E 72 PHE 0.013 0.001 PHE A 383 TYR 0.011 0.001 TYR C 173 ARG 0.003 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8831 (m) REVERT: C 202 THR cc_start: 0.9277 (m) cc_final: 0.8854 (p) REVERT: D 535 MET cc_start: 0.7991 (mpp) cc_final: 0.7549 (mtm) REVERT: A 75 VAL cc_start: 0.8727 (t) cc_final: 0.8507 (m) REVERT: A 217 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: A 432 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: B 655 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8741 (mtpt) REVERT: E 46 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7951 (mtmt) REVERT: E 123 THR cc_start: 0.8565 (p) cc_final: 0.8307 (m) REVERT: E 151 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7765 (ptt90) REVERT: E 194 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8963 (tp) REVERT: E 217 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7519 (t80) REVERT: E 492 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7488 (mt-10) REVERT: F 625 ASN cc_start: 0.8467 (m110) cc_final: 0.8226 (m-40) outliers start: 37 outliers final: 24 residues processed: 234 average time/residue: 0.2735 time to fit residues: 95.2288 Evaluate side-chains 226 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 141 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: C 33 ASN D 640 GLN D 652 GLN B 577 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15973 Z= 0.177 Angle : 0.548 7.841 21732 Z= 0.277 Chirality : 0.044 0.301 2781 Planarity : 0.004 0.054 2662 Dihedral : 6.280 59.959 3956 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.47 % Allowed : 15.10 % Favored : 82.43 % 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: -0.09 (0.20), residues: 1642 helix: 0.31 (0.26), residues: 398 sheet: 0.80 (0.24), residues: 412 loop : -0.65 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.003 0.001 HIS E 105 PHE 0.011 0.001 PHE A 383 TYR 0.020 0.001 TYR E 435 ARG 0.006 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8856 (m) REVERT: C 202 THR cc_start: 0.9308 (m) cc_final: 0.8861 (p) REVERT: D 535 MET cc_start: 0.8012 (mpp) cc_final: 0.7613 (mtm) REVERT: A 217 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: A 432 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: B 540 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: B 586 TYR cc_start: 0.9195 (t80) cc_final: 0.8977 (t80) REVERT: B 655 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8757 (mtpt) REVERT: E 123 THR cc_start: 0.8564 (p) cc_final: 0.8316 (m) REVERT: E 151 ARG cc_start: 0.8091 (ptm160) cc_final: 0.7753 (ptt90) REVERT: E 194 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8939 (tp) REVERT: E 217 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7555 (t80) REVERT: E 492 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7615 (mt-10) outliers start: 37 outliers final: 21 residues processed: 225 average time/residue: 0.2738 time to fit residues: 91.2693 Evaluate side-chains 221 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 640 GLN D 652 GLN B 543 ASN B 577 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15973 Z= 0.270 Angle : 0.595 10.330 21732 Z= 0.298 Chirality : 0.047 0.588 2781 Planarity : 0.004 0.056 2662 Dihedral : 6.394 58.097 3956 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.67 % Allowed : 14.96 % Favored : 82.36 % 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: -0.09 (0.20), residues: 1642 helix: 0.36 (0.27), residues: 392 sheet: 0.75 (0.24), residues: 418 loop : -0.65 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 35 HIS 0.004 0.001 HIS C 105 PHE 0.010 0.002 PHE A 383 TYR 0.020 0.002 TYR E 435 ARG 0.004 0.000 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8907 (m) REVERT: C 202 THR cc_start: 0.9348 (m) cc_final: 0.8892 (p) REVERT: A 217 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: A 432 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: B 540 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: B 586 TYR cc_start: 0.9236 (t80) cc_final: 0.8997 (t80) REVERT: B 655 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8735 (mtpt) REVERT: E 46 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7724 (mtmt) REVERT: E 151 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7757 (ptt90) REVERT: E 194 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8972 (tp) REVERT: E 217 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7655 (t80) outliers start: 40 outliers final: 30 residues processed: 215 average time/residue: 0.2822 time to fit residues: 90.3085 Evaluate side-chains 223 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN D 652 GLN B 577 GLN E 33 ASN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15973 Z= 0.424 Angle : 0.708 8.672 21732 Z= 0.352 Chirality : 0.049 0.535 2781 Planarity : 0.005 0.063 2662 Dihedral : 7.065 59.686 3956 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.47 % Allowed : 15.50 % Favored : 82.03 % 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: -0.44 (0.20), residues: 1642 helix: 0.12 (0.26), residues: 378 sheet: 0.41 (0.24), residues: 419 loop : -0.80 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 35 HIS 0.006 0.001 HIS E 72 PHE 0.014 0.002 PHE C 317 TYR 0.022 0.002 TYR E 435 ARG 0.006 0.001 ARG D 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.8914 (m) REVERT: C 202 THR cc_start: 0.9402 (m) cc_final: 0.8920 (p) REVERT: A 217 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: A 432 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: B 540 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: B 586 TYR cc_start: 0.9322 (t80) cc_final: 0.9053 (t80) REVERT: B 655 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8853 (mtpt) outliers start: 37 outliers final: 29 residues processed: 196 average time/residue: 0.2730 time to fit residues: 78.6658 Evaluate side-chains 197 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN B 543 ASN B 577 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103345 restraints weight = 29558.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106215 restraints weight = 16322.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108124 restraints weight = 11003.106| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15973 Z= 0.169 Angle : 0.550 7.407 21732 Z= 0.280 Chirality : 0.044 0.420 2781 Planarity : 0.004 0.055 2662 Dihedral : 6.022 58.345 3956 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.87 % Allowed : 16.30 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1642 helix: 0.36 (0.27), residues: 396 sheet: 0.62 (0.24), residues: 412 loop : -0.79 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 35 HIS 0.003 0.001 HIS C 105 PHE 0.011 0.001 PHE A 383 TYR 0.018 0.001 TYR E 435 ARG 0.004 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.80 seconds wall clock time: 54 minutes 31.15 seconds (3271.15 seconds total)