Starting phenix.real_space_refine on Fri Feb 16 17:36:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/02_2024/7t73_25732_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/02_2024/7t73_25732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/02_2024/7t73_25732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/02_2024/7t73_25732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/02_2024/7t73_25732_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/02_2024/7t73_25732_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.120 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 107 5.16 5 C 9994 2.51 5 N 2660 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A PHE 93": "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 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 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "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 TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 621": "OE1" <-> "OE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 621": "OE1" <-> "OE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16010 Number of models: 1 Model: "" Number of chains: 28 Chain: "H" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1046 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 801 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3458 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 23, 'TRANS': 417} Chain breaks: 2 Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3392 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 2 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3458 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 23, 'TRANS': 417} Chain breaks: 2 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.07, per 1000 atoms: 0.57 Number of scatterers: 16010 At special positions: 0 Unit cell: (129.95, 128.8, 156.4, 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 107 16.00 O 3249 8.00 N 2660 7.00 C 9994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.19 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.17 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.18 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.23 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.14 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.09 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 D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 7 " " MAN V 4 " - " MAN V 5 " ALPHA1-6 " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 276 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 88 " " NAG C 610 " - " ASN C 339 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E1001 " - " ASN E 197 " " NAG E1002 " - " ASN E 301 " " NAG E1003 " - " ASN E 448 " " NAG E1004 " - " ASN E 276 " " NAG E1005 " - " ASN E 392 " " NAG E1006 " - " ASN E 88 " " NAG E1007 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 160 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN E 156 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 332 " " NAG U 1 " - " ASN E 386 " " NAG V 1 " - " ASN E 160 " Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 2.7 seconds 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 32 sheets defined 21.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.720A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 476 through 482 removed outlier: 4.717A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.273A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 530 through 543 removed outlier: 4.136A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 628 through 635 removed outlier: 3.618A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 649 removed outlier: 3.597A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 661 removed outlier: 4.509A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 removed outlier: 3.627A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (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 351 removed outlier: 3.878A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (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 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.743A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.846A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) 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 341 through 352 removed outlier: 3.550A pdb=" N VAL E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 347 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 476 through 485 removed outlier: 4.574A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 536 removed outlier: 4.951A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 542 No H-bonds generated for 'chain 'D' and resid 539 through 542' Processing helix chain 'D' and resid 573 through 595 removed outlier: 3.762A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' 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 649 removed outlier: 3.596A pdb=" N TYR D 643 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 646 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 653 No H-bonds generated for 'chain 'D' and resid 651 through 653' Processing helix chain 'D' and resid 655 through 661 removed outlier: 3.512A pdb=" N LEU D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.276A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 530 through 543 removed outlier: 3.799A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 removed outlier: 3.575A pdb=" N ALA F 578 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS F 585 " --> pdb=" O ALA F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 624 No H-bonds generated for 'chain 'F' and resid 621 through 624' Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 649 removed outlier: 4.295A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 661 removed outlier: 4.219A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 17 through 22 Processing sheet with id= B, first strand: chain 'H' and resid 100K through 103 removed outlier: 3.542A pdb=" N THR H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.960A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.695A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.594A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= G, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= H, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'A' and resid 130 through 132 removed outlier: 4.231A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= K, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= L, first strand: chain 'A' and resid 413 through 417 removed outlier: 6.474A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 374 through 378 Processing sheet with id= N, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.698A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= P, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.752A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= R, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.601A pdb=" N THR C 132 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= T, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.182A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 413 through 417 removed outlier: 3.798A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.419A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.545A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= Y, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= Z, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.532A pdb=" N GLN E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 160 through 162 Processing sheet with id= AC, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AD, first strand: chain 'E' and resid 271 through 274 Processing sheet with id= AE, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.886A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.702A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1128 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: 5.42 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.32: 3006 1.32 - 1.49: 6620 1.49 - 1.66: 6556 1.66 - 1.83: 107 1.83 - 2.00: 34 Bond restraints: 16323 Sorted by residual: bond pdb=" CA SER E 174 " pdb=" CB SER E 174 " ideal model delta sigma weight residual 1.533 1.377 0.156 1.60e-02 3.91e+03 9.47e+01 bond pdb=" CA SER E 158 " pdb=" CB SER E 158 " ideal model delta sigma weight residual 1.532 1.388 0.144 1.58e-02 4.01e+03 8.31e+01 bond pdb=" C LEU E 175 " pdb=" O LEU E 175 " ideal model delta sigma weight residual 1.236 1.146 0.090 1.21e-02 6.83e+03 5.53e+01 bond pdb=" CB ILE L 106 " pdb=" CG1 ILE L 106 " ideal model delta sigma weight residual 1.530 1.674 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C SER E 158 " pdb=" O SER E 158 " ideal model delta sigma weight residual 1.235 1.158 0.078 1.12e-02 7.97e+03 4.80e+01 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 88.52 - 103.34: 225 103.34 - 118.15: 13032 118.15 - 132.97: 8869 132.97 - 147.79: 50 147.79 - 162.61: 4 Bond angle restraints: 22180 Sorted by residual: angle pdb=" C ASN E 156 " pdb=" CA ASN E 156 " pdb=" CB ASN E 156 " ideal model delta sigma weight residual 110.22 88.52 21.70 1.67e+00 3.59e-01 1.69e+02 angle pdb=" C2 NAG U 1 " pdb=" N2 NAG U 1 " pdb=" C7 NAG U 1 " ideal model delta sigma weight residual 124.56 162.61 -38.05 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG A 609 " pdb=" N2 NAG A 609 " pdb=" C7 NAG A 609 " ideal model delta sigma weight residual 124.56 161.28 -36.72 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.09 -35.53 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG A 603 " pdb=" N2 NAG A 603 " pdb=" C7 NAG A 603 " ideal model delta sigma weight residual 124.56 158.89 -34.33 3.00e+00 1.11e-01 1.31e+02 ... (remaining 22175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 10343 21.90 - 43.80: 288 43.80 - 65.70: 93 65.70 - 87.60: 48 87.60 - 109.50: 28 Dihedral angle restraints: 10800 sinusoidal: 5313 harmonic: 5487 Sorted by residual: dihedral pdb=" C ASN E 156 " pdb=" N ASN E 156 " pdb=" CA ASN E 156 " pdb=" CB ASN E 156 " ideal model delta harmonic sigma weight residual -122.60 -93.57 -29.03 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" CB CYS D 598 " pdb=" SG CYS D 598 " pdb=" SG CYS D 604 " pdb=" CB CYS D 604 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 169.05 -76.05 1 1.00e+01 1.00e-02 7.29e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 2578 0.307 - 0.614: 140 0.614 - 0.922: 1 0.922 - 1.229: 0 1.229 - 1.536: 1 Chirality restraints: 2720 Sorted by residual: chirality pdb=" C1 MAN V 4 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 4.99e+02 chirality pdb=" C1 MAN V 6 " pdb=" O6 MAN V 4 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.60e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 2717 not shown) Planarity restraints: 2786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.372 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C7 NAG N 1 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.561 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 703 " -0.345 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG D 703 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG D 703 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG D 703 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG D 703 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " 0.339 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B 701 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " -0.496 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " 0.056 2.00e-02 2.50e+03 ... (remaining 2783 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 1 2.20 - 2.87: 5541 2.87 - 3.55: 20439 3.55 - 4.22: 38400 4.22 - 4.90: 59520 Nonbonded interactions: 123901 Sorted by model distance: nonbonded pdb=" OG SER F 613 " pdb=" C1 NAG F 701 " model vdw 1.521 3.470 nonbonded pdb=" O5 NAG B 702 " pdb=" O6 NAG B 702 " model vdw 2.217 2.432 nonbonded pdb=" OG SER F 613 " pdb=" O5 NAG F 701 " model vdw 2.244 2.440 nonbonded pdb=" O5 NAG N 1 " pdb=" O6 NAG N 1 " model vdw 2.262 2.432 nonbonded pdb=" O ASN E 136 " pdb=" CB ASN E 136 " model vdw 2.268 2.752 ... (remaining 123896 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 32 through 57 or resid 74 through 501 or resid 601 through \ 607)) selection = (chain 'C' and (resid 32 through 501 or resid 601 through 607)) selection = (chain 'E' and (resid 32 through 57 or resid 74 through 501 or resid 1001 throug \ h 1007)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'R' } 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: 1.270 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: 5.440 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 45.250 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.190 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: 0.010 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: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.021 0.190 16323 Z= 1.342 Angle : 1.921 38.047 22180 Z= 1.219 Chirality : 0.145 1.536 2720 Planarity : 0.018 0.317 2735 Dihedral : 13.611 109.497 7160 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.80 % Allowed : 3.48 % Favored : 95.72 % Rotamer: Outliers : 1.56 % Allowed : 1.38 % Favored : 97.07 % Cbeta Deviations : 0.79 % 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: -0.60 (0.18), residues: 1867 helix: -1.13 (0.24), residues: 355 sheet: -0.07 (0.23), residues: 477 loop : -0.16 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.009 TRP E 479 HIS 0.011 0.002 HIS D 585 PHE 0.062 0.006 PHE E 159 TYR 0.048 0.007 TYR C 191 ARG 0.014 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 503 time to evaluate : 1.661 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: H 107 THR cc_start: 0.3110 (t) cc_final: 0.2275 (m) REVERT: L 48 ILE cc_start: 0.7032 (mt) cc_final: 0.6814 (tt) REVERT: A 35 TRP cc_start: 0.8285 (m100) cc_final: 0.7597 (m-10) REVERT: A 104 MET cc_start: 0.9451 (ttt) cc_final: 0.9239 (ttp) REVERT: A 287 GLN cc_start: 0.7552 (tt0) cc_final: 0.7110 (mm110) REVERT: A 426 MET cc_start: 0.7700 (ttt) cc_final: 0.7230 (tpt) REVERT: B 626 MET cc_start: 0.7680 (mtp) cc_final: 0.7475 (mtt) REVERT: B 632 ASP cc_start: 0.8720 (t70) cc_final: 0.8425 (t70) REVERT: C 82 GLN cc_start: 0.7248 (mt0) cc_final: 0.7044 (tt0) REVERT: C 97 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7570 (tptp) REVERT: C 129 LEU cc_start: 0.9191 (mt) cc_final: 0.8966 (mp) REVERT: C 156 ASN cc_start: 0.9315 (t0) cc_final: 0.8820 (t0) REVERT: C 168 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7289 (mtmm) REVERT: C 217 TYR cc_start: 0.8640 (m-80) cc_final: 0.8223 (m-80) REVERT: C 492 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8317 (mt-10) REVERT: C 498 PRO cc_start: 0.9499 (OUTLIER) cc_final: 0.8849 (Cg_exo) REVERT: E 194 ILE cc_start: 0.8929 (tp) cc_final: 0.8430 (tt) REVERT: E 264 SER cc_start: 0.8447 (t) cc_final: 0.7786 (m) REVERT: E 282 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8947 (mmmt) REVERT: D 522 PHE cc_start: 0.9223 (t80) cc_final: 0.8954 (t80) REVERT: D 536 THR cc_start: 0.7947 (p) cc_final: 0.7438 (t) REVERT: D 610 TRP cc_start: 0.8843 (t-100) cc_final: 0.8381 (t-100) REVERT: D 616 ASN cc_start: 0.7344 (p0) cc_final: 0.7143 (p0) REVERT: D 623 TRP cc_start: 0.8951 (m100) cc_final: 0.8032 (m100) REVERT: D 643 TYR cc_start: 0.8532 (m-10) cc_final: 0.8275 (m-80) REVERT: F 543 ASN cc_start: 0.8597 (m-40) cc_final: 0.8221 (m-40) REVERT: F 601 LYS cc_start: 0.8900 (mttt) cc_final: 0.8666 (mmtp) outliers start: 26 outliers final: 8 residues processed: 520 average time/residue: 0.2910 time to fit residues: 218.8231 Evaluate side-chains 279 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 270 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 498 PRO Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain F residue 615 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 89 GLN A 103 GLN A 170 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 85 HIS C 234 ASN C 300 ASN C 363 GLN E 136 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16323 Z= 0.269 Angle : 0.790 10.346 22180 Z= 0.400 Chirality : 0.052 0.300 2720 Planarity : 0.005 0.035 2735 Dihedral : 10.931 85.819 3663 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Rotamer: Outliers : 3.53 % Allowed : 11.13 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1867 helix: -0.45 (0.28), residues: 339 sheet: -0.26 (0.23), residues: 483 loop : -0.41 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 479 HIS 0.006 0.001 HIS C 85 PHE 0.027 0.003 PHE E 233 TYR 0.021 0.002 TYR C 217 ARG 0.006 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 310 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6459 (tp) REVERT: L 47 LEU cc_start: 0.4568 (mt) cc_final: 0.3899 (mt) REVERT: A 35 TRP cc_start: 0.7931 (m100) cc_final: 0.7563 (m-10) REVERT: A 106 GLU cc_start: 0.8774 (tt0) cc_final: 0.8226 (tp30) REVERT: A 120 VAL cc_start: 0.9215 (m) cc_final: 0.8991 (p) REVERT: A 287 GLN cc_start: 0.7452 (tt0) cc_final: 0.7042 (mm-40) REVERT: B 628 TRP cc_start: 0.9231 (m100) cc_final: 0.8326 (m100) REVERT: B 640 GLN cc_start: 0.8706 (mp10) cc_final: 0.8347 (mp10) REVERT: B 648 GLU cc_start: 0.7841 (tp30) cc_final: 0.7350 (tp30) REVERT: C 112 TRP cc_start: 0.8386 (t-100) cc_final: 0.8067 (t-100) REVERT: C 168 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7261 (mtmm) REVERT: C 210 PHE cc_start: 0.8314 (m-80) cc_final: 0.7753 (m-80) REVERT: C 278 THR cc_start: 0.9061 (p) cc_final: 0.8654 (t) REVERT: C 426 MET cc_start: 0.7166 (mmm) cc_final: 0.6941 (mmm) REVERT: E 113 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8792 (t0) REVERT: E 194 ILE cc_start: 0.8720 (tp) cc_final: 0.8394 (tt) REVERT: E 264 SER cc_start: 0.8526 (t) cc_final: 0.8222 (m) REVERT: E 282 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8971 (mmmt) REVERT: E 426 MET cc_start: 0.8079 (tpt) cc_final: 0.7874 (tpt) REVERT: E 475 MET cc_start: 0.7309 (mtp) cc_final: 0.6932 (ttt) REVERT: D 522 PHE cc_start: 0.9296 (t80) cc_final: 0.9017 (t80) REVERT: D 542 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7806 (mmm-85) REVERT: D 592 LEU cc_start: 0.8665 (tp) cc_final: 0.8299 (mt) REVERT: D 610 TRP cc_start: 0.8924 (t-100) cc_final: 0.8443 (t-100) REVERT: D 653 GLN cc_start: 0.7948 (mp10) cc_final: 0.7641 (mp10) REVERT: F 543 ASN cc_start: 0.8443 (m-40) cc_final: 0.7890 (t0) REVERT: F 621 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7771 (mt-10) REVERT: F 641 ILE cc_start: 0.8878 (mp) cc_final: 0.8665 (tp) outliers start: 59 outliers final: 34 residues processed: 354 average time/residue: 0.2767 time to fit residues: 146.8229 Evaluate side-chains 287 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 183 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN A 103 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 653 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS F 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16323 Z= 0.238 Angle : 0.689 11.050 22180 Z= 0.352 Chirality : 0.048 0.267 2720 Planarity : 0.004 0.040 2735 Dihedral : 9.172 71.195 3651 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.48 % Favored : 96.36 % Rotamer: Outliers : 3.23 % Allowed : 13.05 % Favored : 83.72 % 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: -0.82 (0.19), residues: 1867 helix: -0.55 (0.27), residues: 363 sheet: -0.20 (0.23), residues: 479 loop : -0.63 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 103 HIS 0.005 0.001 HIS A 72 PHE 0.021 0.002 PHE H 27 TYR 0.018 0.002 TYR L 86 ARG 0.007 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 258 time to evaluate : 1.781 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: H 78 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6485 (tp) REVERT: H 82 MET cc_start: 0.5758 (mmt) cc_final: 0.3703 (tpp) REVERT: H 100 ASP cc_start: 0.7023 (t0) cc_final: 0.6386 (t0) REVERT: H 100 TYR cc_start: 0.5801 (m-10) cc_final: 0.5102 (m-10) REVERT: L 47 LEU cc_start: 0.4052 (mt) cc_final: 0.3829 (mp) REVERT: A 35 TRP cc_start: 0.7850 (m100) cc_final: 0.7587 (m-10) REVERT: A 78 ASP cc_start: 0.7684 (t0) cc_final: 0.7312 (p0) REVERT: A 106 GLU cc_start: 0.8868 (tt0) cc_final: 0.8236 (tp30) REVERT: A 168 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8010 (ttpt) REVERT: A 287 GLN cc_start: 0.7644 (tt0) cc_final: 0.7038 (mm-40) REVERT: B 640 GLN cc_start: 0.8706 (mp10) cc_final: 0.8354 (mp10) REVERT: B 648 GLU cc_start: 0.7911 (tp30) cc_final: 0.7453 (tp30) REVERT: B 653 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6836 (pp30) REVERT: C 97 LYS cc_start: 0.8225 (tptp) cc_final: 0.7848 (tptp) REVERT: C 112 TRP cc_start: 0.8286 (t-100) cc_final: 0.8059 (t-100) REVERT: C 177 TYR cc_start: 0.8407 (m-80) cc_final: 0.8071 (m-80) REVERT: C 210 PHE cc_start: 0.8376 (m-80) cc_final: 0.7826 (m-80) REVERT: C 258 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: C 278 THR cc_start: 0.9041 (p) cc_final: 0.8638 (t) REVERT: E 113 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8687 (t0) REVERT: E 194 ILE cc_start: 0.8630 (tp) cc_final: 0.8285 (tt) REVERT: E 426 MET cc_start: 0.8225 (tpt) cc_final: 0.7971 (tpt) REVERT: D 542 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.7804 (mmm-85) REVERT: D 592 LEU cc_start: 0.8780 (tp) cc_final: 0.8424 (mt) REVERT: F 530 MET cc_start: 0.8395 (mtm) cc_final: 0.8093 (mtp) REVERT: F 543 ASN cc_start: 0.8520 (m-40) cc_final: 0.8060 (t0) REVERT: F 546 SER cc_start: 0.6821 (p) cc_final: 0.6421 (m) REVERT: F 621 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7825 (mt-10) outliers start: 54 outliers final: 37 residues processed: 296 average time/residue: 0.2982 time to fit residues: 132.0920 Evaluate side-chains 266 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16323 Z= 0.236 Angle : 0.670 13.090 22180 Z= 0.340 Chirality : 0.048 0.326 2720 Planarity : 0.004 0.040 2735 Dihedral : 7.524 60.298 3650 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 3.89 % Allowed : 14.18 % Favored : 81.93 % 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: -0.85 (0.19), residues: 1867 helix: -0.43 (0.27), residues: 354 sheet: -0.21 (0.24), residues: 473 loop : -0.71 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 103 HIS 0.004 0.001 HIS A 216 PHE 0.018 0.002 PHE E 93 TYR 0.018 0.002 TYR A 217 ARG 0.004 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 245 time to evaluate : 1.711 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: H 82 MET cc_start: 0.5633 (mmt) cc_final: 0.3700 (tpt) REVERT: H 100 ASP cc_start: 0.7032 (t0) cc_final: 0.6661 (t0) REVERT: A 35 TRP cc_start: 0.7814 (m100) cc_final: 0.7580 (m-10) REVERT: A 78 ASP cc_start: 0.7793 (t0) cc_final: 0.7371 (p0) REVERT: A 106 GLU cc_start: 0.8956 (tt0) cc_final: 0.8310 (tp30) REVERT: A 150 MET cc_start: 0.7958 (mmt) cc_final: 0.7197 (mmt) REVERT: A 168 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8148 (ttpt) REVERT: A 287 GLN cc_start: 0.7869 (tt0) cc_final: 0.7121 (mm-40) REVERT: B 648 GLU cc_start: 0.7982 (tp30) cc_final: 0.7514 (tp30) REVERT: B 653 GLN cc_start: 0.7558 (pp30) cc_final: 0.7250 (pp30) REVERT: C 177 TYR cc_start: 0.8439 (m-80) cc_final: 0.8088 (m-80) REVERT: C 210 PHE cc_start: 0.8381 (m-80) cc_final: 0.7900 (m-80) REVERT: C 465 THR cc_start: 0.6794 (m) cc_final: 0.6354 (p) REVERT: E 194 ILE cc_start: 0.8674 (tp) cc_final: 0.8308 (tt) REVERT: D 542 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8073 (mmm-85) REVERT: D 592 LEU cc_start: 0.8808 (tp) cc_final: 0.8490 (mt) REVERT: F 530 MET cc_start: 0.8378 (mtm) cc_final: 0.8018 (mtp) REVERT: F 543 ASN cc_start: 0.8540 (m-40) cc_final: 0.8098 (t0) REVERT: F 546 SER cc_start: 0.7067 (p) cc_final: 0.6687 (m) REVERT: F 621 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7738 (mt-10) outliers start: 65 outliers final: 45 residues processed: 289 average time/residue: 0.2778 time to fit residues: 119.1938 Evaluate side-chains 269 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16323 Z= 0.236 Angle : 0.655 13.809 22180 Z= 0.336 Chirality : 0.048 0.384 2720 Planarity : 0.004 0.042 2735 Dihedral : 6.894 57.076 3649 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 4.07 % Allowed : 14.72 % Favored : 81.21 % 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: -0.92 (0.19), residues: 1867 helix: -0.45 (0.27), residues: 363 sheet: -0.10 (0.24), residues: 466 loop : -0.86 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 103 HIS 0.004 0.001 HIS E 216 PHE 0.029 0.002 PHE H 29 TYR 0.018 0.002 TYR L 86 ARG 0.004 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 244 time to evaluate : 1.928 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: H 82 MET cc_start: 0.5689 (mmt) cc_final: 0.3651 (tpt) REVERT: H 100 ASP cc_start: 0.7178 (t0) cc_final: 0.6787 (t0) REVERT: L 47 LEU cc_start: 0.3922 (mt) cc_final: 0.3566 (mp) REVERT: L 62 PHE cc_start: 0.6255 (m-80) cc_final: 0.6018 (m-80) REVERT: A 35 TRP cc_start: 0.7878 (m100) cc_final: 0.7624 (m-10) REVERT: A 78 ASP cc_start: 0.7894 (t0) cc_final: 0.7417 (p0) REVERT: A 150 MET cc_start: 0.7982 (mmt) cc_final: 0.7241 (mmt) REVERT: A 168 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8198 (ttpt) REVERT: A 287 GLN cc_start: 0.7626 (tt0) cc_final: 0.7067 (mm-40) REVERT: A 426 MET cc_start: 0.7190 (ttp) cc_final: 0.5801 (tpt) REVERT: B 621 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: B 626 MET cc_start: 0.7706 (mtp) cc_final: 0.7470 (mtt) REVERT: B 648 GLU cc_start: 0.8029 (tp30) cc_final: 0.7621 (tp30) REVERT: C 95 MET cc_start: 0.7399 (mtp) cc_final: 0.5917 (ptp) REVERT: C 97 LYS cc_start: 0.8166 (tptp) cc_final: 0.7838 (tptp) REVERT: C 114 GLN cc_start: 0.8664 (mm110) cc_final: 0.8212 (mt0) REVERT: C 177 TYR cc_start: 0.8509 (m-80) cc_final: 0.8131 (m-80) REVERT: C 258 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: C 465 THR cc_start: 0.6374 (m) cc_final: 0.5969 (p) REVERT: D 542 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.7871 (mmm-85) REVERT: D 639 THR cc_start: 0.8803 (p) cc_final: 0.8505 (m) REVERT: F 530 MET cc_start: 0.8342 (mtm) cc_final: 0.8019 (mtp) REVERT: F 543 ASN cc_start: 0.8563 (m-40) cc_final: 0.8146 (t0) REVERT: F 546 SER cc_start: 0.7139 (p) cc_final: 0.6874 (m) outliers start: 68 outliers final: 51 residues processed: 285 average time/residue: 0.2779 time to fit residues: 116.8290 Evaluate side-chains 279 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 226 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 0.0060 chunk 94 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN C 170 GLN E 289 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16323 Z= 0.208 Angle : 0.629 14.488 22180 Z= 0.323 Chirality : 0.047 0.301 2720 Planarity : 0.004 0.041 2735 Dihedral : 6.531 55.209 3648 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 3.77 % Allowed : 15.44 % Favored : 80.79 % 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: -0.85 (0.19), residues: 1867 helix: -0.34 (0.27), residues: 363 sheet: -0.03 (0.23), residues: 498 loop : -0.87 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 103 HIS 0.003 0.001 HIS A 216 PHE 0.016 0.002 PHE E 93 TYR 0.025 0.001 TYR A 484 ARG 0.005 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 251 time to evaluate : 1.718 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: H 82 MET cc_start: 0.5664 (mmt) cc_final: 0.3678 (tpt) REVERT: H 100 ASP cc_start: 0.7206 (t0) cc_final: 0.6412 (t0) REVERT: H 100 TYR cc_start: 0.5820 (m-10) cc_final: 0.4857 (m-10) REVERT: L 86 TYR cc_start: 0.7358 (m-10) cc_final: 0.6980 (m-10) REVERT: A 78 ASP cc_start: 0.7875 (t0) cc_final: 0.7427 (p0) REVERT: A 150 MET cc_start: 0.8007 (mmt) cc_final: 0.7492 (mmt) REVERT: A 168 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8213 (ttpt) REVERT: A 287 GLN cc_start: 0.7706 (tt0) cc_final: 0.7056 (mm-40) REVERT: A 426 MET cc_start: 0.7266 (ttp) cc_final: 0.5531 (tpp) REVERT: B 648 GLU cc_start: 0.7989 (tp30) cc_final: 0.7586 (tp30) REVERT: C 88 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7232 (p0) REVERT: C 95 MET cc_start: 0.7446 (mtp) cc_final: 0.6742 (ptp) REVERT: C 114 GLN cc_start: 0.8641 (mm110) cc_final: 0.8214 (mt0) REVERT: C 177 TYR cc_start: 0.8443 (m-80) cc_final: 0.8094 (m-80) REVERT: C 465 THR cc_start: 0.6257 (m) cc_final: 0.5853 (p) REVERT: E 54 CYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5992 (t) REVERT: E 486 TYR cc_start: 0.8095 (m-80) cc_final: 0.7871 (m-80) REVERT: D 522 PHE cc_start: 0.9208 (t80) cc_final: 0.8962 (t80) REVERT: D 542 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: D 639 THR cc_start: 0.8806 (p) cc_final: 0.8563 (m) REVERT: F 530 MET cc_start: 0.8308 (mtm) cc_final: 0.7946 (mtp) REVERT: F 543 ASN cc_start: 0.8567 (m-40) cc_final: 0.8133 (t0) REVERT: F 546 SER cc_start: 0.6963 (p) cc_final: 0.6736 (m) outliers start: 63 outliers final: 48 residues processed: 291 average time/residue: 0.2871 time to fit residues: 123.0490 Evaluate side-chains 286 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 236 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 0.0470 chunk 102 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 101 optimal weight: 0.3980 chunk 180 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 83 optimal weight: 0.0060 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100HHIS B 653 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16323 Z= 0.180 Angle : 0.608 14.124 22180 Z= 0.310 Chirality : 0.047 0.373 2720 Planarity : 0.004 0.040 2735 Dihedral : 6.056 54.502 3648 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 3.65 % Allowed : 15.74 % Favored : 80.61 % 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 (0.19), residues: 1867 helix: 0.07 (0.28), residues: 345 sheet: -0.11 (0.23), residues: 508 loop : -0.84 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 103 HIS 0.004 0.001 HIS A 216 PHE 0.013 0.001 PHE E 93 TYR 0.021 0.001 TYR A 484 ARG 0.006 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 251 time to evaluate : 1.835 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: H 82 MET cc_start: 0.5695 (mmt) cc_final: 0.3787 (tpt) REVERT: H 100 ASP cc_start: 0.7170 (t0) cc_final: 0.6856 (t0) REVERT: A 78 ASP cc_start: 0.7891 (t0) cc_final: 0.7377 (p0) REVERT: A 150 MET cc_start: 0.7799 (mmt) cc_final: 0.7333 (mmt) REVERT: A 168 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8222 (ttpt) REVERT: A 287 GLN cc_start: 0.7623 (tt0) cc_final: 0.7000 (mm-40) REVERT: A 426 MET cc_start: 0.7241 (ttp) cc_final: 0.5621 (tpt) REVERT: A 469 ARG cc_start: 0.9231 (ptp-170) cc_final: 0.8887 (ptp-170) REVERT: B 596 TRP cc_start: 0.8106 (m-10) cc_final: 0.7761 (m-10) REVERT: B 648 GLU cc_start: 0.7922 (tp30) cc_final: 0.7524 (tp30) REVERT: C 88 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7239 (p0) REVERT: C 95 MET cc_start: 0.7355 (mtp) cc_final: 0.5961 (ptp) REVERT: C 97 LYS cc_start: 0.8177 (tptp) cc_final: 0.7598 (mtpp) REVERT: C 114 GLN cc_start: 0.8626 (mm110) cc_final: 0.8219 (mt0) REVERT: C 132 THR cc_start: 0.9218 (p) cc_final: 0.8968 (t) REVERT: C 177 TYR cc_start: 0.8402 (m-80) cc_final: 0.8063 (m-80) REVERT: C 465 THR cc_start: 0.6119 (m) cc_final: 0.5736 (p) REVERT: E 486 TYR cc_start: 0.8328 (m-80) cc_final: 0.8072 (m-80) REVERT: D 639 THR cc_start: 0.8916 (p) cc_final: 0.8581 (m) REVERT: D 640 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7761 (tp-100) REVERT: F 530 MET cc_start: 0.8124 (mtm) cc_final: 0.7757 (mtp) REVERT: F 542 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7797 (mtm-85) REVERT: F 543 ASN cc_start: 0.8572 (m-40) cc_final: 0.8139 (t0) outliers start: 61 outliers final: 41 residues processed: 288 average time/residue: 0.2810 time to fit residues: 119.2686 Evaluate side-chains 276 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 0.3980 chunk 71 optimal weight: 0.3980 chunk 107 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 653 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16323 Z= 0.253 Angle : 0.645 13.867 22180 Z= 0.328 Chirality : 0.049 0.377 2720 Planarity : 0.004 0.039 2735 Dihedral : 6.328 59.024 3648 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % Rotamer: Outliers : 3.35 % Allowed : 16.34 % Favored : 80.31 % 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: -0.76 (0.19), residues: 1867 helix: 0.07 (0.28), residues: 351 sheet: -0.21 (0.23), residues: 512 loop : -0.82 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 103 HIS 0.005 0.001 HIS E 216 PHE 0.021 0.002 PHE L 62 TYR 0.024 0.002 TYR A 484 ARG 0.006 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 247 time to evaluate : 1.572 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: H 82 MET cc_start: 0.5545 (mmt) cc_final: 0.3494 (tpt) REVERT: H 100 ASP cc_start: 0.7273 (t0) cc_final: 0.6923 (t0) REVERT: A 78 ASP cc_start: 0.7953 (t0) cc_final: 0.7689 (t0) REVERT: A 150 MET cc_start: 0.7836 (mmt) cc_final: 0.7245 (mmt) REVERT: A 168 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8383 (ttpt) REVERT: A 287 GLN cc_start: 0.7759 (tt0) cc_final: 0.7062 (mm-40) REVERT: A 426 MET cc_start: 0.7443 (ttp) cc_final: 0.5761 (tpt) REVERT: A 469 ARG cc_start: 0.9213 (ptp-170) cc_final: 0.8866 (ptp90) REVERT: B 648 GLU cc_start: 0.7902 (tp30) cc_final: 0.7512 (tp30) REVERT: C 95 MET cc_start: 0.7278 (mtp) cc_final: 0.6096 (ptp) REVERT: C 114 GLN cc_start: 0.8672 (mm110) cc_final: 0.8247 (mt0) REVERT: C 168 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7621 (mtpt) REVERT: C 177 TYR cc_start: 0.8498 (m-80) cc_final: 0.8154 (m-80) REVERT: C 465 THR cc_start: 0.6069 (m) cc_final: 0.5686 (p) REVERT: E 486 TYR cc_start: 0.8380 (m-80) cc_final: 0.8113 (m-80) REVERT: D 640 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7679 (tp-100) REVERT: D 643 TYR cc_start: 0.8568 (m-10) cc_final: 0.7981 (m-80) REVERT: F 543 ASN cc_start: 0.8499 (m-40) cc_final: 0.8200 (t0) outliers start: 56 outliers final: 47 residues processed: 280 average time/residue: 0.2848 time to fit residues: 117.2472 Evaluate side-chains 280 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN B 653 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN D 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16323 Z= 0.238 Angle : 0.639 13.681 22180 Z= 0.327 Chirality : 0.048 0.319 2720 Planarity : 0.004 0.042 2735 Dihedral : 6.203 57.702 3648 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 3.41 % Allowed : 16.40 % Favored : 80.19 % 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: -0.80 (0.19), residues: 1867 helix: 0.20 (0.28), residues: 352 sheet: -0.31 (0.23), residues: 512 loop : -0.86 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP H 47 HIS 0.004 0.001 HIS A 216 PHE 0.021 0.002 PHE L 62 TYR 0.025 0.002 TYR A 484 ARG 0.006 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 1.869 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: H 47 TRP cc_start: 0.3392 (t60) cc_final: 0.3106 (t60) REVERT: H 82 MET cc_start: 0.5527 (mmt) cc_final: 0.3676 (tpp) REVERT: H 100 ASP cc_start: 0.8945 (p0) cc_final: 0.8561 (p0) REVERT: H 100 ASP cc_start: 0.7303 (t0) cc_final: 0.6954 (t0) REVERT: A 78 ASP cc_start: 0.7980 (t0) cc_final: 0.7719 (t0) REVERT: A 150 MET cc_start: 0.7881 (mmt) cc_final: 0.7282 (mmt) REVERT: A 168 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8454 (ttpt) REVERT: A 426 MET cc_start: 0.7426 (ttp) cc_final: 0.5770 (tpt) REVERT: A 469 ARG cc_start: 0.9084 (ptp-170) cc_final: 0.8855 (ptp90) REVERT: B 648 GLU cc_start: 0.8046 (tp30) cc_final: 0.7650 (tp30) REVERT: C 88 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7290 (p0) REVERT: C 95 MET cc_start: 0.7270 (mtp) cc_final: 0.6097 (ptp) REVERT: C 114 GLN cc_start: 0.8695 (mm110) cc_final: 0.8247 (mt0) REVERT: C 168 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7638 (mtpt) REVERT: C 177 TYR cc_start: 0.8497 (m-80) cc_final: 0.8165 (m-80) REVERT: C 465 THR cc_start: 0.5975 (m) cc_final: 0.5614 (p) REVERT: E 486 TYR cc_start: 0.8421 (m-80) cc_final: 0.8071 (m-80) REVERT: D 640 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7597 (tp-100) REVERT: D 643 TYR cc_start: 0.8522 (m-10) cc_final: 0.7948 (m-80) REVERT: F 543 ASN cc_start: 0.8547 (m-40) cc_final: 0.8228 (t0) outliers start: 57 outliers final: 50 residues processed: 273 average time/residue: 0.2923 time to fit residues: 117.5985 Evaluate side-chains 280 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 229 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 45 TRP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16323 Z= 0.380 Angle : 0.731 13.620 22180 Z= 0.371 Chirality : 0.050 0.294 2720 Planarity : 0.004 0.054 2735 Dihedral : 6.506 55.893 3648 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 3.41 % Allowed : 16.76 % Favored : 79.83 % 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: -1.01 (0.19), residues: 1867 helix: -0.05 (0.28), residues: 364 sheet: -0.40 (0.23), residues: 506 loop : -1.00 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.007 0.001 HIS E 216 PHE 0.029 0.003 PHE L 98 TYR 0.029 0.002 TYR A 484 ARG 0.006 0.001 ARG D 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 1.806 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: H 47 TRP cc_start: 0.3282 (t60) cc_final: 0.3035 (t60) REVERT: H 82 MET cc_start: 0.5722 (mmt) cc_final: 0.3893 (tpt) REVERT: H 100 ASP cc_start: 0.8942 (p0) cc_final: 0.8551 (p0) REVERT: H 100 ASP cc_start: 0.7392 (t0) cc_final: 0.7161 (t0) REVERT: L 38 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7254 (tp40) REVERT: A 78 ASP cc_start: 0.8053 (t0) cc_final: 0.7797 (t0) REVERT: A 104 MET cc_start: 0.8117 (ttp) cc_final: 0.7296 (ttp) REVERT: A 150 MET cc_start: 0.7935 (mmt) cc_final: 0.7322 (mmt) REVERT: A 168 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8582 (ttpt) REVERT: A 426 MET cc_start: 0.7665 (ttp) cc_final: 0.5777 (tpp) REVERT: A 469 ARG cc_start: 0.9179 (ptp-170) cc_final: 0.8940 (ptp90) REVERT: B 648 GLU cc_start: 0.7989 (tp30) cc_final: 0.7779 (tp30) REVERT: C 88 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7286 (p0) REVERT: C 96 TRP cc_start: 0.8591 (m-90) cc_final: 0.8370 (m100) REVERT: C 114 GLN cc_start: 0.8737 (mm110) cc_final: 0.8155 (mt0) REVERT: C 168 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7686 (mtmt) REVERT: C 465 THR cc_start: 0.6012 (m) cc_final: 0.5647 (p) REVERT: E 327 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7471 (mtm-85) REVERT: E 486 TYR cc_start: 0.8575 (m-80) cc_final: 0.8188 (m-80) REVERT: D 639 THR cc_start: 0.8843 (p) cc_final: 0.8515 (m) REVERT: D 640 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7556 (tp-100) outliers start: 57 outliers final: 49 residues processed: 264 average time/residue: 0.2927 time to fit residues: 113.2065 Evaluate side-chains 267 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 217 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 45 TRP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 190 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119655 restraints weight = 24636.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119406 restraints weight = 28163.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120850 restraints weight = 25465.243| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16323 Z= 0.226 Angle : 0.648 13.639 22180 Z= 0.330 Chirality : 0.048 0.281 2720 Planarity : 0.004 0.041 2735 Dihedral : 6.299 55.371 3648 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 3.17 % Allowed : 17.24 % Favored : 79.59 % 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: -0.93 (0.19), residues: 1867 helix: 0.17 (0.29), residues: 352 sheet: -0.47 (0.23), residues: 516 loop : -0.93 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 631 HIS 0.005 0.001 HIS A 216 PHE 0.019 0.002 PHE L 62 TYR 0.027 0.001 TYR A 484 ARG 0.008 0.000 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3285.67 seconds wall clock time: 60 minutes 46.98 seconds (3646.98 seconds total)