Starting phenix.real_space_refine on Sat Mar 16 22:41:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/03_2024/7l8g_23233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/03_2024/7l8g_23233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/03_2024/7l8g_23233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/03_2024/7l8g_23233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/03_2024/7l8g_23233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/03_2024/7l8g_23233_updated.pdb" } resolution = 4.3 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= 0.002 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 102 5.16 5 C 9826 2.51 5 N 2656 2.21 5 O 3218 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 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15802 Number of models: 1 Model: "" Number of chains: 39 Chain: "C" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3512 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3499 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 952 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3497 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "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: 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: "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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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 Time building chain proxies: 8.94, per 1000 atoms: 0.57 Number of scatterers: 15802 At special positions: 0 Unit cell: (130.81, 125.66, 145.23, 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 102 16.00 O 3218 8.00 N 2656 7.00 C 9826 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 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.07 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.11 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 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 G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA R 3 " - " MAN R 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 701 " - " ASN A 276 " " NAG A 702 " - " ASN A 386 " " NAG A 703 " - " ASN A 363 " " NAG A 704 " - " ASN A 234 " " NAG A 705 " - " ASN A 133 " " NAG A 706 " - " ASN A 289 " " NAG A 707 " - " ASN A 339 " " NAG A 708 " - " ASN A 355 " " NAG A 709 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 276 " " NAG C 703 " - " ASN C 386 " " NAG C 704 " - " ASN C 363 " " NAG C 705 " - " ASN C 133 " " NAG C 706 " - " ASN C 301 " " NAG C 707 " - " ASN C 289 " " NAG C 708 " - " ASN C 339 " " NAG C 709 " - " ASN C 355 " " NAG C 710 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 701 " - " ASN E 160 " " NAG E 702 " - " ASN E 276 " " NAG E 703 " - " ASN E 386 " " NAG E 704 " - " ASN E 363 " " NAG E 705 " - " ASN E 234 " " NAG E 706 " - " ASN E 133 " " NAG E 707 " - " ASN E 301 " " NAG E 708 " - " ASN E 289 " " NAG E 709 " - " ASN E 339 " " NAG E 710 " - " ASN E 355 " " NAG E 711 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 88 " " NAG P 1 " - " ASN C 241 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN E 262 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 295 " " NAG U 1 " - " ASN E 197 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 241 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 197 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 88 " " NAG e 1 " - " ASN A 241 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 160 " Time building additional restraints: 6.95 Conformation dependent library (CDL) restraints added in 2.6 seconds 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 30 sheets defined 24.8% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 100 through 117 removed outlier: 4.846A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 4.371A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 476 through 485 removed outlier: 3.742A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 545 removed outlier: 3.961A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 540 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 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 639 through 660 removed outlier: 4.515A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 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 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.618A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.138A 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 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 475 through 478 Processing helix chain 'E' and resid 480 through 485 removed outlier: 6.314A pdb=" N LYS E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 Processing helix chain 'F' and resid 532 through 540 removed outlier: 3.914A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 Processing helix chain 'F' and resid 619 through 625 removed outlier: 4.428A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 640 through 657 removed outlier: 3.855A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) 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 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.611A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 476 through 485 removed outlier: 4.423A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.926A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 537 through 545 removed outlier: 4.026A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 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 639 through 659 removed outlier: 3.917A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) 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 Processing sheet with id= C, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'C' and resid 169 through 177 Processing sheet with id= F, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.530A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.441A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.595A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.370A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= K, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= M, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= N, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.728A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.475A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 301 through 303 removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 305 through 308 Processing sheet with id= T, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= U, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= V, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= X, first strand: chain 'A' and resid 169 through 177 Processing sheet with id= Y, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.468A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.283A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.711A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.615A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.009A pdb=" N UNK L 100 " --> pdb=" O UNK L 11 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 85 through 87 removed outlier: 6.214A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.08 Time building geometry restraints manager: 7.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4070 1.33 - 1.47: 4938 1.47 - 1.61: 6917 1.61 - 1.75: 24 1.75 - 1.89: 124 Bond restraints: 16073 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.52e+01 bond pdb=" CB LEU D 661 " pdb=" CG LEU D 661 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.303 0.067 1.10e-02 8.26e+03 3.69e+01 bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 16068 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.67: 371 105.67 - 112.76: 8606 112.76 - 119.84: 5990 119.84 - 126.93: 6664 126.93 - 134.02: 232 Bond angle restraints: 21863 Sorted by residual: angle pdb=" N THR C 320 " pdb=" CA THR C 320 " pdb=" C THR C 320 " ideal model delta sigma weight residual 112.54 122.84 -10.30 1.22e+00 6.72e-01 7.13e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.01e+00 9.80e-01 7.11e+01 angle pdb=" N ILE E 424 " pdb=" CA ILE E 424 " pdb=" C ILE E 424 " ideal model delta sigma weight residual 108.11 119.66 -11.55 1.40e+00 5.10e-01 6.81e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.56 -8.00 1.01e+00 9.80e-01 6.28e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.70 101.84 8.86 1.22e+00 6.72e-01 5.28e+01 ... (remaining 21858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 10583 21.32 - 42.65: 218 42.65 - 63.97: 73 63.97 - 85.29: 31 85.29 - 106.61: 15 Dihedral angle restraints: 10920 sinusoidal: 5403 harmonic: 5517 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -132.02 46.02 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -41.57 -44.43 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -130.05 44.05 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 10917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 2441 0.247 - 0.494: 349 0.494 - 0.740: 9 0.740 - 0.987: 0 0.987 - 1.234: 1 Chirality restraints: 2800 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 -2.63 0.23 2.00e-02 2.50e+03 1.27e+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 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 ... (remaining 2797 not shown) Planarity restraints: 2734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " -0.350 2.00e-02 2.50e+03 3.01e-01 1.14e+03 pdb=" C7 NAG F 702 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.117 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " 0.347 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C 702 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 708 " 0.331 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG A 708 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A 708 " 0.050 2.00e-02 2.50e+03 pdb=" N2 NAG A 708 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG A 708 " 0.198 2.00e-02 2.50e+03 ... (remaining 2731 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5191 2.86 - 3.37: 14822 3.37 - 3.88: 26543 3.88 - 4.39: 30773 4.39 - 4.90: 47205 Nonbonded interactions: 124534 Sorted by model distance: nonbonded pdb=" N LEU F 523 " pdb=" OE1 GLN F 540 " model vdw 2.354 2.520 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.399 2.520 nonbonded pdb=" OD1 ASP E 368 " pdb=" N LEU E 369 " model vdw 2.424 2.520 nonbonded pdb=" NZ LYS A 335 " pdb=" OD2 ASP A 412 " model vdw 2.439 2.520 nonbonded pdb=" N PRO E 437 " pdb=" O PRO E 437 " model vdw 2.439 2.496 ... (remaining 124529 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 505 or resid 701 through 709)) selection = (chain 'C' and (resid 33 through 58 or resid 66 through 397 or resid 411 through \ 505 or resid 701 through 709)) selection = (chain 'E' and (resid 33 through 58 or resid 66 through 505 or resid 702 through \ 710)) } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 569 through 660 or resid 701 thro \ ugh 703)) selection = (chain 'D' and (resid 520 through 546 or resid 569 through 660 or resid 701 thro \ ugh 703)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'Y' } ncs_group { reference = (chain 'H' and resid 11 through 110) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.150 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 44.190 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.240 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 0.131 16073 Z= 1.382 Angle : 1.756 14.048 21863 Z= 1.115 Chirality : 0.156 1.234 2800 Planarity : 0.016 0.301 2670 Dihedral : 11.312 106.613 7233 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1659 helix: -0.69 (0.23), residues: 421 sheet: 1.04 (0.23), residues: 438 loop : 0.94 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.010 TRP C 35 HIS 0.017 0.003 HIS C 374 PHE 0.035 0.006 PHE E 353 TYR 0.041 0.008 TYR E 173 ARG 0.006 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8791 (m-80) cc_final: 0.8410 (m-80) REVERT: C 453 ILE cc_start: 0.9234 (mt) cc_final: 0.8903 (tt) REVERT: D 543 ASN cc_start: 0.9127 (m-40) cc_final: 0.8904 (m110) REVERT: D 571 TRP cc_start: 0.6645 (t60) cc_final: 0.6196 (t60) REVERT: D 588 ARG cc_start: 0.9167 (mmm160) cc_final: 0.8924 (tpp-160) REVERT: D 630 GLN cc_start: 0.9336 (mt0) cc_final: 0.9134 (mt0) REVERT: D 639 THR cc_start: 0.8967 (p) cc_final: 0.8737 (p) REVERT: E 129 LEU cc_start: 0.9176 (mt) cc_final: 0.8942 (mt) REVERT: E 166 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8370 (mtp85) REVERT: E 338 TRP cc_start: 0.8699 (t-100) cc_final: 0.8492 (t-100) REVERT: F 523 LEU cc_start: 0.9265 (mt) cc_final: 0.8915 (mt) REVERT: F 536 THR cc_start: 0.8788 (p) cc_final: 0.8553 (t) REVERT: F 590 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8752 (tm-30) REVERT: F 591 GLN cc_start: 0.9440 (tt0) cc_final: 0.8910 (tt0) REVERT: F 630 GLN cc_start: 0.9445 (mt0) cc_final: 0.8952 (mt0) REVERT: F 634 GLU cc_start: 0.8622 (tp30) cc_final: 0.8275 (tt0) REVERT: F 638 TYR cc_start: 0.7927 (m-80) cc_final: 0.7584 (m-80) REVERT: F 648 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8950 (tm-30) REVERT: F 656 ASN cc_start: 0.9152 (m-40) cc_final: 0.8781 (m-40) REVERT: A 47 ASP cc_start: 0.8793 (m-30) cc_final: 0.8557 (p0) REVERT: B 536 THR cc_start: 0.8870 (p) cc_final: 0.8641 (p) REVERT: B 584 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8904 (tm-30) REVERT: B 585 HIS cc_start: 0.8873 (m-70) cc_final: 0.8597 (m-70) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.3034 time to fit residues: 172.6881 Evaluate side-chains 213 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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: 2.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 114 GLN C 302 ASN C 352 HIS D 591 GLN E 203 GLN ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16073 Z= 0.254 Angle : 0.745 10.540 21863 Z= 0.381 Chirality : 0.049 0.326 2800 Planarity : 0.004 0.030 2670 Dihedral : 8.641 86.027 4041 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.40 % Allowed : 2.38 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1659 helix: 0.57 (0.26), residues: 394 sheet: 0.75 (0.22), residues: 460 loop : 0.44 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 623 HIS 0.010 0.001 HIS A 249 PHE 0.017 0.002 PHE C 53 TYR 0.025 0.002 TYR B 643 ARG 0.005 0.001 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8596 (m-80) cc_final: 0.8312 (m-80) REVERT: C 104 MET cc_start: 0.9089 (mmp) cc_final: 0.8774 (mmp) REVERT: C 150 MET cc_start: 0.7875 (mmm) cc_final: 0.7575 (mmt) REVERT: C 426 MET cc_start: 0.8848 (tpt) cc_final: 0.8632 (tpp) REVERT: C 434 MET cc_start: 0.9168 (ttp) cc_final: 0.8946 (ttp) REVERT: D 626 MET cc_start: 0.8022 (mtp) cc_final: 0.7502 (mtp) REVERT: D 639 THR cc_start: 0.8909 (p) cc_final: 0.8669 (p) REVERT: D 653 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9052 (mm110) REVERT: E 104 MET cc_start: 0.9047 (ttt) cc_final: 0.8750 (ttt) REVERT: E 195 ASN cc_start: 0.8191 (t0) cc_final: 0.7915 (t0) REVERT: E 338 TRP cc_start: 0.8632 (t-100) cc_final: 0.8365 (t-100) REVERT: E 368 ASP cc_start: 0.8507 (p0) cc_final: 0.8185 (p0) REVERT: F 522 PHE cc_start: 0.8499 (t80) cc_final: 0.8236 (t80) REVERT: F 530 MET cc_start: 0.9107 (mtt) cc_final: 0.8788 (mtt) REVERT: F 535 MET cc_start: 0.8440 (mpp) cc_final: 0.8017 (mpp) REVERT: F 589 ASP cc_start: 0.9307 (m-30) cc_final: 0.8979 (m-30) REVERT: F 599 SER cc_start: 0.9311 (p) cc_final: 0.8965 (m) REVERT: F 626 MET cc_start: 0.7923 (tpp) cc_final: 0.6839 (tpp) REVERT: F 630 GLN cc_start: 0.9501 (mt0) cc_final: 0.9145 (mt0) REVERT: F 634 GLU cc_start: 0.8692 (tp30) cc_final: 0.8451 (tt0) REVERT: A 53 PHE cc_start: 0.8173 (m-10) cc_final: 0.7914 (m-10) REVERT: A 104 MET cc_start: 0.8448 (tpt) cc_final: 0.6896 (tpt) REVERT: A 161 MET cc_start: 0.9111 (tpp) cc_final: 0.8579 (tpp) REVERT: A 166 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8485 (ttm110) REVERT: A 217 TYR cc_start: 0.8209 (m-10) cc_final: 0.7735 (m-10) REVERT: A 359 ILE cc_start: 0.8225 (mt) cc_final: 0.7968 (mm) REVERT: A 368 ASP cc_start: 0.8503 (p0) cc_final: 0.8166 (p0) REVERT: B 523 LEU cc_start: 0.9120 (mt) cc_final: 0.8591 (mt) REVERT: B 584 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8975 (tm-30) REVERT: B 586 TYR cc_start: 0.9247 (t80) cc_final: 0.9043 (t80) REVERT: B 626 MET cc_start: 0.8013 (tpp) cc_final: 0.7659 (tpp) REVERT: B 630 GLN cc_start: 0.9190 (mt0) cc_final: 0.8891 (mt0) REVERT: B 654 GLU cc_start: 0.9261 (tp30) cc_final: 0.9053 (tp30) outliers start: 6 outliers final: 0 residues processed: 283 average time/residue: 0.2875 time to fit residues: 118.2829 Evaluate side-chains 191 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 46 optimal weight: 0.0970 chunk 170 optimal weight: 40.0000 chunk 183 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 168 optimal weight: 40.0000 chunk 57 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 overall best weight: 3.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 293 GLN C 374 HIS D 575 GLN E 183 GLN E 287 GLN A 80 ASN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 570 HIS B 585 HIS B 651 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 16073 Z= 0.374 Angle : 0.749 11.374 21863 Z= 0.381 Chirality : 0.048 0.319 2800 Planarity : 0.004 0.041 2670 Dihedral : 7.916 77.431 4041 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.33 % Allowed : 3.24 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1659 helix: 0.29 (0.26), residues: 412 sheet: 0.47 (0.22), residues: 488 loop : 0.08 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 479 HIS 0.007 0.002 HIS A 105 PHE 0.030 0.003 PHE D 522 TYR 0.022 0.002 TYR C 217 ARG 0.007 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 214 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8830 (m-80) cc_final: 0.8369 (m-80) REVERT: C 150 MET cc_start: 0.8002 (mmm) cc_final: 0.7746 (mmp) REVERT: C 475 MET cc_start: 0.9058 (mmp) cc_final: 0.8734 (mmm) REVERT: C 478 ASN cc_start: 0.9057 (m110) cc_final: 0.8831 (m110) REVERT: D 542 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8348 (mtm-85) REVERT: D 584 GLU cc_start: 0.9066 (pp20) cc_final: 0.8819 (tm-30) REVERT: D 626 MET cc_start: 0.8291 (mtp) cc_final: 0.7821 (mtp) REVERT: D 631 TRP cc_start: 0.8574 (t-100) cc_final: 0.8117 (t-100) REVERT: E 95 MET cc_start: 0.9022 (ptm) cc_final: 0.8546 (ppp) REVERT: E 195 ASN cc_start: 0.8098 (t0) cc_final: 0.7687 (t0) REVERT: E 368 ASP cc_start: 0.8588 (p0) cc_final: 0.8302 (p0) REVERT: F 523 LEU cc_start: 0.9245 (mt) cc_final: 0.8950 (mt) REVERT: F 535 MET cc_start: 0.8342 (mpp) cc_final: 0.8067 (mpp) REVERT: A 150 MET cc_start: 0.9137 (mmm) cc_final: 0.8908 (mpp) REVERT: A 166 ARG cc_start: 0.8790 (ttm110) cc_final: 0.8587 (ttm110) REVERT: A 359 ILE cc_start: 0.8274 (mt) cc_final: 0.8068 (mm) REVERT: A 368 ASP cc_start: 0.8195 (p0) cc_final: 0.7835 (p0) REVERT: B 584 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8953 (tm-30) REVERT: B 601 LYS cc_start: 0.9280 (pttm) cc_final: 0.8922 (ptpp) REVERT: B 626 MET cc_start: 0.8085 (tpp) cc_final: 0.7780 (tpp) REVERT: B 630 GLN cc_start: 0.9144 (mt0) cc_final: 0.8756 (mt0) REVERT: B 654 GLU cc_start: 0.9321 (tp30) cc_final: 0.9016 (tp30) REVERT: B 657 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8352 (tm-30) outliers start: 5 outliers final: 1 residues processed: 217 average time/residue: 0.2764 time to fit residues: 88.4727 Evaluate side-chains 161 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 30.0000 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 170 optimal weight: 40.0000 chunk 180 optimal weight: 50.0000 chunk 89 optimal weight: 0.6980 chunk 161 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16073 Z= 0.249 Angle : 0.619 10.537 21863 Z= 0.316 Chirality : 0.046 0.302 2800 Planarity : 0.003 0.034 2670 Dihedral : 7.452 71.770 4041 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.13 % Allowed : 1.72 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1659 helix: 0.65 (0.27), residues: 404 sheet: 0.40 (0.22), residues: 468 loop : -0.05 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.007 0.001 HIS A 249 PHE 0.019 0.002 PHE D 522 TYR 0.017 0.001 TYR C 217 ARG 0.003 0.000 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8818 (m-80) cc_final: 0.8211 (m-80) REVERT: D 542 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8370 (mtm-85) REVERT: D 574 LYS cc_start: 0.9190 (pttp) cc_final: 0.8833 (pttp) REVERT: D 626 MET cc_start: 0.8409 (mtp) cc_final: 0.8017 (mtp) REVERT: D 630 GLN cc_start: 0.9179 (mt0) cc_final: 0.8943 (mt0) REVERT: E 95 MET cc_start: 0.9027 (ptm) cc_final: 0.7807 (ppp) REVERT: E 161 MET cc_start: 0.8218 (tpp) cc_final: 0.7851 (tpt) REVERT: E 195 ASN cc_start: 0.7981 (t0) cc_final: 0.7676 (t0) REVERT: E 368 ASP cc_start: 0.8581 (p0) cc_final: 0.8141 (p0) REVERT: E 432 GLN cc_start: 0.7997 (pm20) cc_final: 0.7710 (pm20) REVERT: F 535 MET cc_start: 0.8536 (mpp) cc_final: 0.8247 (mpp) REVERT: F 589 ASP cc_start: 0.8996 (m-30) cc_final: 0.8747 (m-30) REVERT: F 591 GLN cc_start: 0.9368 (tt0) cc_final: 0.9002 (tt0) REVERT: F 626 MET cc_start: 0.8104 (tpp) cc_final: 0.7589 (tpp) REVERT: A 150 MET cc_start: 0.9190 (mmm) cc_final: 0.8942 (mpp) REVERT: A 217 TYR cc_start: 0.8747 (m-10) cc_final: 0.8007 (m-10) REVERT: A 359 ILE cc_start: 0.8222 (mt) cc_final: 0.8003 (mm) REVERT: A 368 ASP cc_start: 0.8231 (p0) cc_final: 0.7749 (p0) REVERT: B 584 GLU cc_start: 0.9368 (mt-10) cc_final: 0.8962 (tm-30) REVERT: B 601 LYS cc_start: 0.9293 (pttm) cc_final: 0.8959 (ptpp) REVERT: B 620 SER cc_start: 0.8201 (m) cc_final: 0.7922 (p) REVERT: B 626 MET cc_start: 0.8139 (tpp) cc_final: 0.7797 (tpp) REVERT: B 630 GLN cc_start: 0.9134 (mt0) cc_final: 0.8786 (mt0) REVERT: B 654 GLU cc_start: 0.9282 (tp30) cc_final: 0.9038 (tp30) REVERT: B 657 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8421 (tm-30) outliers start: 2 outliers final: 0 residues processed: 217 average time/residue: 0.2843 time to fit residues: 92.3123 Evaluate side-chains 159 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 195 ASN D 575 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS B 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 16073 Z= 0.429 Angle : 0.775 19.339 21863 Z= 0.388 Chirality : 0.049 0.320 2800 Planarity : 0.004 0.039 2670 Dihedral : 7.899 68.969 4041 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.07 % Allowed : 2.45 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1659 helix: 0.19 (0.27), residues: 405 sheet: 0.37 (0.23), residues: 438 loop : -0.37 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 479 HIS 0.006 0.002 HIS A 85 PHE 0.019 0.003 PHE A 317 TYR 0.028 0.002 TYR C 217 ARG 0.007 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8923 (m-80) cc_final: 0.8230 (m-80) REVERT: C 475 MET cc_start: 0.9004 (mmp) cc_final: 0.8792 (mmm) REVERT: C 478 ASN cc_start: 0.9209 (m110) cc_final: 0.8876 (m110) REVERT: D 542 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8478 (ttm110) REVERT: D 626 MET cc_start: 0.8492 (mtp) cc_final: 0.8023 (mtp) REVERT: D 630 GLN cc_start: 0.9161 (mt0) cc_final: 0.8960 (mt0) REVERT: E 195 ASN cc_start: 0.8223 (t0) cc_final: 0.7975 (t0) REVERT: E 368 ASP cc_start: 0.8592 (p0) cc_final: 0.8273 (p0) REVERT: F 535 MET cc_start: 0.8482 (mpp) cc_final: 0.8202 (mpp) REVERT: F 589 ASP cc_start: 0.9085 (m-30) cc_final: 0.8832 (m-30) REVERT: F 630 GLN cc_start: 0.9387 (mt0) cc_final: 0.9111 (mt0) REVERT: F 648 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8751 (tm-30) REVERT: A 359 ILE cc_start: 0.8496 (mt) cc_final: 0.8253 (mm) REVERT: A 368 ASP cc_start: 0.8095 (p0) cc_final: 0.7614 (p0) REVERT: A 425 ASN cc_start: 0.9246 (m110) cc_final: 0.9029 (m-40) REVERT: B 584 GLU cc_start: 0.9379 (mt-10) cc_final: 0.8977 (tm-30) REVERT: B 601 LYS cc_start: 0.9360 (pttm) cc_final: 0.8989 (ptpp) REVERT: B 620 SER cc_start: 0.8298 (m) cc_final: 0.7705 (p) REVERT: B 625 ASN cc_start: 0.8876 (m-40) cc_final: 0.8136 (m110) REVERT: B 626 MET cc_start: 0.8170 (tpp) cc_final: 0.7818 (tpp) REVERT: B 630 GLN cc_start: 0.9120 (mt0) cc_final: 0.8898 (mt0) REVERT: B 654 GLU cc_start: 0.9284 (tp30) cc_final: 0.9035 (tp30) REVERT: B 657 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8434 (tm-30) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.2802 time to fit residues: 79.2369 Evaluate side-chains 146 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 180 optimal weight: 50.0000 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN F 616 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 16073 Z= 0.426 Angle : 0.757 16.364 21863 Z= 0.384 Chirality : 0.049 0.317 2800 Planarity : 0.004 0.040 2670 Dihedral : 8.110 65.210 4041 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1659 helix: 0.06 (0.27), residues: 402 sheet: 0.21 (0.24), residues: 419 loop : -0.54 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 571 HIS 0.011 0.002 HIS A 105 PHE 0.023 0.003 PHE C 53 TYR 0.031 0.002 TYR C 217 ARG 0.006 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8983 (m-80) cc_final: 0.8137 (m-80) REVERT: C 478 ASN cc_start: 0.9186 (m110) cc_final: 0.8904 (m110) REVERT: D 542 ARG cc_start: 0.8750 (mtp180) cc_final: 0.8447 (ttm110) REVERT: D 574 LYS cc_start: 0.9162 (pttp) cc_final: 0.8881 (pttp) REVERT: D 626 MET cc_start: 0.8571 (mtp) cc_final: 0.8071 (mtp) REVERT: E 161 MET cc_start: 0.8506 (tpp) cc_final: 0.8150 (tpt) REVERT: E 195 ASN cc_start: 0.8156 (t0) cc_final: 0.7953 (t0) REVERT: E 368 ASP cc_start: 0.8596 (p0) cc_final: 0.8264 (p0) REVERT: F 535 MET cc_start: 0.8532 (mpp) cc_final: 0.8234 (mpp) REVERT: F 589 ASP cc_start: 0.9107 (m-30) cc_final: 0.8785 (m-30) REVERT: F 591 GLN cc_start: 0.9394 (tt0) cc_final: 0.9075 (tt0) REVERT: A 359 ILE cc_start: 0.8577 (mt) cc_final: 0.8337 (mm) REVERT: B 584 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8934 (tm-30) REVERT: B 626 MET cc_start: 0.8138 (tpp) cc_final: 0.7725 (mmm) REVERT: B 630 GLN cc_start: 0.9069 (mt0) cc_final: 0.8427 (mt0) REVERT: B 654 GLU cc_start: 0.9261 (tp30) cc_final: 0.8651 (tp30) REVERT: B 657 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8252 (tm-30) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2705 time to fit residues: 75.2840 Evaluate side-chains 140 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 40.0000 chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 180 optimal weight: 50.0000 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS D 575 GLN D 591 GLN E 478 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 16073 Z= 0.419 Angle : 0.758 15.858 21863 Z= 0.381 Chirality : 0.050 0.306 2800 Planarity : 0.004 0.039 2670 Dihedral : 8.250 62.879 4041 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1659 helix: 0.06 (0.27), residues: 398 sheet: 0.08 (0.24), residues: 431 loop : -0.66 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 631 HIS 0.008 0.002 HIS A 249 PHE 0.017 0.002 PHE C 53 TYR 0.021 0.002 TYR A 217 ARG 0.005 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8983 (m-80) cc_final: 0.8099 (m-80) REVERT: C 478 ASN cc_start: 0.9138 (m110) cc_final: 0.8780 (m110) REVERT: D 542 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8423 (ttm110) REVERT: D 574 LYS cc_start: 0.9134 (pttp) cc_final: 0.8926 (pttp) REVERT: E 104 MET cc_start: 0.9084 (ttt) cc_final: 0.8835 (ttt) REVERT: E 195 ASN cc_start: 0.8194 (t0) cc_final: 0.7980 (t0) REVERT: F 530 MET cc_start: 0.8696 (pmm) cc_final: 0.8467 (pmm) REVERT: F 535 MET cc_start: 0.8572 (mpp) cc_final: 0.8257 (mpp) REVERT: F 589 ASP cc_start: 0.9075 (m-30) cc_final: 0.8767 (m-30) REVERT: F 599 SER cc_start: 0.9439 (m) cc_final: 0.9223 (p) REVERT: F 638 TYR cc_start: 0.8131 (m-80) cc_final: 0.7920 (m-80) REVERT: A 359 ILE cc_start: 0.8633 (mt) cc_final: 0.8385 (mm) REVERT: A 452 LEU cc_start: 0.9411 (mt) cc_final: 0.9100 (mt) REVERT: A 475 MET cc_start: 0.9220 (tpt) cc_final: 0.8834 (tpp) REVERT: B 584 GLU cc_start: 0.9440 (mt-10) cc_final: 0.8971 (tm-30) REVERT: B 635 ILE cc_start: 0.9228 (pt) cc_final: 0.8999 (pt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2784 time to fit residues: 77.2685 Evaluate side-chains 134 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS C 188 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16073 Z= 0.204 Angle : 0.638 16.035 21863 Z= 0.324 Chirality : 0.047 0.291 2800 Planarity : 0.003 0.038 2670 Dihedral : 7.511 60.834 4041 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.07 % Allowed : 0.59 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1659 helix: 0.35 (0.27), residues: 406 sheet: 0.19 (0.24), residues: 429 loop : -0.50 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 112 HIS 0.006 0.001 HIS C 249 PHE 0.021 0.002 PHE C 53 TYR 0.021 0.001 TYR C 217 ARG 0.004 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8946 (m-80) cc_final: 0.7993 (m-80) REVERT: D 542 ARG cc_start: 0.8749 (mtp180) cc_final: 0.8444 (ttm110) REVERT: D 626 MET cc_start: 0.8193 (mtp) cc_final: 0.7892 (mtm) REVERT: E 95 MET cc_start: 0.9119 (ptm) cc_final: 0.8397 (ppp) REVERT: F 530 MET cc_start: 0.8695 (pmm) cc_final: 0.8425 (pmm) REVERT: F 599 SER cc_start: 0.9467 (m) cc_final: 0.9175 (p) REVERT: A 359 ILE cc_start: 0.8477 (mt) cc_final: 0.8207 (mm) REVERT: A 452 LEU cc_start: 0.9381 (mt) cc_final: 0.9122 (mt) REVERT: A 475 MET cc_start: 0.9122 (tpt) cc_final: 0.8734 (tpp) REVERT: B 584 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8931 (tm-30) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.2680 time to fit residues: 83.8940 Evaluate side-chains 145 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 575 GLN ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16073 Z= 0.312 Angle : 0.679 15.585 21863 Z= 0.344 Chirality : 0.048 0.295 2800 Planarity : 0.004 0.040 2670 Dihedral : 7.587 59.339 4041 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1659 helix: 0.17 (0.27), residues: 408 sheet: 0.15 (0.23), residues: 450 loop : -0.63 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 479 HIS 0.006 0.001 HIS D 585 PHE 0.020 0.002 PHE C 53 TYR 0.013 0.001 TYR C 217 ARG 0.004 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9000 (m-80) cc_final: 0.8074 (m-80) REVERT: C 104 MET cc_start: 0.8753 (mmp) cc_final: 0.8362 (mmp) REVERT: C 475 MET cc_start: 0.8629 (mmm) cc_final: 0.8290 (mmm) REVERT: D 542 ARG cc_start: 0.8740 (mtp180) cc_final: 0.8448 (ttm110) REVERT: D 584 GLU cc_start: 0.8967 (pp20) cc_final: 0.8763 (pp20) REVERT: E 95 MET cc_start: 0.9049 (ptm) cc_final: 0.8418 (ppp) REVERT: F 530 MET cc_start: 0.8677 (pmm) cc_final: 0.8417 (pmm) REVERT: F 599 SER cc_start: 0.9451 (m) cc_final: 0.9219 (p) REVERT: F 648 GLU cc_start: 0.9241 (tm-30) cc_final: 0.9003 (tm-30) REVERT: F 654 GLU cc_start: 0.9152 (tp30) cc_final: 0.8920 (tp30) REVERT: A 217 TYR cc_start: 0.8401 (m-10) cc_final: 0.7774 (m-10) REVERT: A 359 ILE cc_start: 0.8538 (mt) cc_final: 0.8278 (mm) REVERT: A 452 LEU cc_start: 0.9359 (mt) cc_final: 0.9061 (mt) REVERT: A 475 MET cc_start: 0.9124 (tpt) cc_final: 0.8742 (tpp) REVERT: B 584 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8928 (tm-30) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2534 time to fit residues: 72.4262 Evaluate side-chains 133 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 30.0000 chunk 108 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 186 optimal weight: 30.0000 chunk 171 optimal weight: 40.0000 chunk 148 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 577 GLN D 630 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 630 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16073 Z= 0.269 Angle : 0.661 15.594 21863 Z= 0.336 Chirality : 0.048 0.288 2800 Planarity : 0.004 0.039 2670 Dihedral : 7.539 57.674 4041 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1659 helix: 0.26 (0.27), residues: 406 sheet: 0.06 (0.24), residues: 441 loop : -0.63 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS C 249 PHE 0.018 0.002 PHE C 53 TYR 0.016 0.001 TYR A 217 ARG 0.004 0.000 ARG F 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9046 (m-80) cc_final: 0.8158 (m-80) REVERT: C 260 LEU cc_start: 0.9424 (mt) cc_final: 0.9202 (mt) REVERT: D 542 ARG cc_start: 0.8782 (mtp180) cc_final: 0.8465 (ttm110) REVERT: E 95 MET cc_start: 0.9037 (ptm) cc_final: 0.8400 (ppp) REVERT: F 530 MET cc_start: 0.8670 (pmm) cc_final: 0.8232 (pmm) REVERT: F 575 GLN cc_start: 0.8965 (pp30) cc_final: 0.8753 (pp30) REVERT: F 599 SER cc_start: 0.9467 (m) cc_final: 0.9265 (p) REVERT: A 217 TYR cc_start: 0.8361 (m-10) cc_final: 0.7778 (m-10) REVERT: A 359 ILE cc_start: 0.8521 (mt) cc_final: 0.8261 (mm) REVERT: A 452 LEU cc_start: 0.9341 (mt) cc_final: 0.9046 (mt) REVERT: A 475 MET cc_start: 0.9129 (tpt) cc_final: 0.8742 (tpp) REVERT: B 584 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8967 (tm-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2533 time to fit residues: 70.3321 Evaluate side-chains 138 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 577 GLN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 630 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.046237 restraints weight = 77888.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.047562 restraints weight = 47359.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.048454 restraints weight = 34290.907| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16073 Z= 0.355 Angle : 0.710 15.275 21863 Z= 0.358 Chirality : 0.048 0.291 2800 Planarity : 0.004 0.039 2670 Dihedral : 7.771 55.824 4041 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1659 helix: 0.13 (0.27), residues: 406 sheet: 0.01 (0.24), residues: 427 loop : -0.77 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 631 HIS 0.005 0.001 HIS A 330 PHE 0.015 0.002 PHE D 522 TYR 0.023 0.002 TYR C 217 ARG 0.004 0.000 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.57 seconds wall clock time: 52 minutes 47.91 seconds (3167.91 seconds total)