Starting phenix.real_space_refine on Fri Feb 16 12:17:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7u_23219/02_2024/7l7u_23219.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7u_23219/02_2024/7l7u_23219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7u_23219/02_2024/7l7u_23219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7u_23219/02_2024/7l7u_23219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7u_23219/02_2024/7l7u_23219.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7u_23219/02_2024/7l7u_23219.pdb" } resolution = 3.8 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= 0.002 sd= 0.010 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 105 5.16 5 C 9504 2.51 5 N 2544 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15258 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "D" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "F" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.20, per 1000 atoms: 0.54 Number of scatterers: 15258 At special positions: 0 Unit cell: (128.8, 125.35, 118.45, 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 105 16.00 O 3105 8.00 N 2544 7.00 C 9504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.09 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=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA O 3 " - " MAN O 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA O 3 " - " MAN O 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 276 " " NAG A 603 " - " ASN A 386 " " NAG A 604 " - " ASN A 363 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 133 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 289 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 386 " " NAG C 604 " - " ASN C 363 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 133 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 289 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 386 " " NAG E 604 " - " ASN E 363 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 133 " " NAG E 607 " - " ASN E 241 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 301 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN C 262 " " NAG P 1 " - " ASN C 448 " " NAG Q 1 " - " ASN C 295 " " NAG R 1 " - " ASN C 197 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 448 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 197 " " NAG a 1 " - " ASN E 156 " " NAG b 1 " - " ASN E 301 " " NAG c 1 " - " ASN E 88 " " NAG d 1 " - " ASN E 332 " Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 2.7 seconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 31.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.021A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.827A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 542 through 556 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.022A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.827A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 542 through 556 Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.021A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.826A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 542 through 556 Processing helix chain 'F' and resid 560 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.911A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.563A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.911A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.562A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.910A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.563A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3638 1.32 - 1.46: 4661 1.46 - 1.59: 7065 1.59 - 1.73: 50 1.73 - 1.86: 126 Bond restraints: 15540 Sorted by residual: bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.640 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" CB LEU D 520 " pdb=" CG LEU D 520 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB PHE A 376 " pdb=" CG PHE A 376 " ideal model delta sigma weight residual 1.502 1.379 0.123 2.30e-02 1.89e+03 2.85e+01 bond pdb=" CB PHE E 376 " pdb=" CG PHE E 376 " ideal model delta sigma weight residual 1.502 1.380 0.122 2.30e-02 1.89e+03 2.83e+01 ... (remaining 15535 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.93: 388 105.93 - 113.00: 8568 113.00 - 120.07: 6066 120.07 - 127.13: 5876 127.13 - 134.20: 204 Bond angle restraints: 21102 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.14 -8.27 1.04e+00 9.25e-01 6.32e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.12 -8.25 1.04e+00 9.25e-01 6.30e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.11 -8.24 1.04e+00 9.25e-01 6.28e+01 angle pdb=" C GLY E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta sigma weight residual 119.76 127.28 -7.52 1.03e+00 9.43e-01 5.33e+01 angle pdb=" C GLY A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta sigma weight residual 119.76 127.25 -7.49 1.03e+00 9.43e-01 5.29e+01 ... (remaining 21097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 10206 21.10 - 42.20: 238 42.20 - 63.30: 71 63.30 - 84.40: 42 84.40 - 105.50: 15 Dihedral angle restraints: 10572 sinusoidal: 5481 harmonic: 5091 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.68 -68.68 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.67 -68.67 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.67 -68.67 1 1.00e+01 1.00e-02 6.11e+01 ... (remaining 10569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1799 0.111 - 0.221: 523 0.221 - 0.332: 210 0.332 - 0.442: 105 0.442 - 0.553: 27 Chirality restraints: 2664 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 ... (remaining 2661 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A 607 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 607 " 0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C 607 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C 607 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C 607 " -0.531 2.00e-02 2.50e+03 pdb=" O7 NAG C 607 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 607 " -0.348 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG E 607 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG E 607 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG E 607 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG E 607 " -0.121 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6283 2.91 - 3.41: 13691 3.41 - 3.90: 25725 3.90 - 4.40: 28847 4.40 - 4.90: 45643 Nonbonded interactions: 120189 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.411 2.496 nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.412 2.496 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.412 2.496 nonbonded pdb=" O3 NAG G 1 " pdb=" O7 NAG G 1 " model vdw 2.432 2.440 nonbonded pdb=" O3 NAG W 1 " pdb=" O7 NAG W 1 " model vdw 2.432 2.440 ... (remaining 120184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 0.010 Normalize map: mean=0, sd=1: 0.300 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: 2.290 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 41.930 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.230 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.023 0.136 15540 Z= 1.432 Angle : 1.685 11.057 21102 Z= 1.095 Chirality : 0.149 0.553 2664 Planarity : 0.019 0.299 2565 Dihedral : 11.592 105.496 7200 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % 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: 0.66 (0.19), residues: 1731 helix: -0.11 (0.21), residues: 480 sheet: 1.31 (0.22), residues: 495 loop : 0.37 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.013 TRP E 479 HIS 0.008 0.003 HIS A 85 PHE 0.019 0.006 PHE A 93 TYR 0.030 0.007 TYR E 217 ARG 0.005 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8354 (mtp) cc_final: 0.8024 (mtp) REVERT: A 140 ASP cc_start: 0.7871 (t0) cc_final: 0.7418 (t0) REVERT: A 179 LEU cc_start: 0.9376 (mt) cc_final: 0.9171 (mt) REVERT: B 523 LEU cc_start: 0.9331 (mt) cc_final: 0.8967 (mt) REVERT: B 534 SER cc_start: 0.8676 (p) cc_final: 0.8343 (p) REVERT: B 543 ASN cc_start: 0.8985 (t0) cc_final: 0.8474 (t0) REVERT: B 564 HIS cc_start: 0.5296 (t70) cc_final: 0.4892 (t-90) REVERT: B 577 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8183 (tt0) REVERT: B 616 ASN cc_start: 0.8382 (p0) cc_final: 0.8158 (p0) REVERT: B 617 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7548 (ttp80) REVERT: B 647 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6715 (mt-10) REVERT: C 100 MET cc_start: 0.8542 (mtp) cc_final: 0.8029 (mtp) REVERT: C 115 SER cc_start: 0.9087 (m) cc_final: 0.8813 (t) REVERT: C 125 LEU cc_start: 0.8791 (tt) cc_final: 0.8516 (tt) REVERT: D 577 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8182 (tt0) REVERT: D 617 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7702 (tpp80) REVERT: D 627 THR cc_start: 0.8270 (p) cc_final: 0.8031 (p) REVERT: E 140 ASP cc_start: 0.7997 (t0) cc_final: 0.7782 (t0) REVERT: F 523 LEU cc_start: 0.9292 (mt) cc_final: 0.8888 (mt) REVERT: F 577 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8073 (tt0) REVERT: F 617 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7776 (tpp80) REVERT: F 637 ASN cc_start: 0.7057 (m-40) cc_final: 0.6848 (m-40) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.2914 time to fit residues: 188.5201 Evaluate side-chains 238 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 103 GLN A 258 GLN B 562 GLN C 85 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN D 656 ASN E 85 HIS E 258 GLN E 478 ASN F 562 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15540 Z= 0.242 Angle : 0.686 10.351 21102 Z= 0.357 Chirality : 0.048 0.194 2664 Planarity : 0.004 0.051 2565 Dihedral : 9.280 82.370 3864 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.10 % Allowed : 9.21 % Favored : 88.70 % 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: 0.97 (0.19), residues: 1731 helix: 1.32 (0.24), residues: 471 sheet: 1.04 (0.24), residues: 465 loop : 0.08 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 479 HIS 0.004 0.001 HIS E 330 PHE 0.019 0.002 PHE E 468 TYR 0.011 0.002 TYR A 384 ARG 0.006 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 266 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8449 (p0) cc_final: 0.8043 (p0) REVERT: A 100 MET cc_start: 0.7969 (mtp) cc_final: 0.7727 (mtp) REVERT: A 125 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8510 (tt) REVERT: A 217 TYR cc_start: 0.8537 (m-80) cc_final: 0.8100 (m-80) REVERT: B 523 LEU cc_start: 0.9311 (mt) cc_final: 0.9004 (mt) REVERT: B 535 MET cc_start: 0.7813 (mmm) cc_final: 0.7560 (mmp) REVERT: B 543 ASN cc_start: 0.9057 (t0) cc_final: 0.8601 (t0) REVERT: B 564 HIS cc_start: 0.5292 (t70) cc_final: 0.4967 (t-90) REVERT: B 615 SER cc_start: 0.8540 (t) cc_final: 0.8233 (m) REVERT: B 632 ASP cc_start: 0.7925 (t0) cc_final: 0.7718 (t0) REVERT: C 115 SER cc_start: 0.9165 (m) cc_final: 0.8864 (t) REVERT: D 523 LEU cc_start: 0.9234 (mt) cc_final: 0.8873 (mt) REVERT: D 564 HIS cc_start: 0.4720 (t-90) cc_final: 0.4185 (t-90) REVERT: D 577 GLN cc_start: 0.8346 (tp-100) cc_final: 0.8054 (tt0) REVERT: D 615 SER cc_start: 0.8464 (t) cc_final: 0.8213 (m) REVERT: D 616 ASN cc_start: 0.8322 (p0) cc_final: 0.7970 (p0) REVERT: D 659 ASP cc_start: 0.7380 (m-30) cc_final: 0.7114 (m-30) REVERT: E 49 GLU cc_start: 0.8760 (pm20) cc_final: 0.8540 (pm20) REVERT: E 100 MET cc_start: 0.7672 (mtm) cc_final: 0.7462 (mtm) REVERT: F 577 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7822 (tt0) REVERT: F 615 SER cc_start: 0.8614 (t) cc_final: 0.8197 (m) REVERT: F 626 MET cc_start: 0.8107 (ttp) cc_final: 0.7763 (ttt) outliers start: 33 outliers final: 14 residues processed: 288 average time/residue: 0.2373 time to fit residues: 105.3050 Evaluate side-chains 215 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 328 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 302 ASN E 302 ASN E 328 GLN F 607 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15540 Z= 0.256 Angle : 0.623 11.650 21102 Z= 0.315 Chirality : 0.046 0.213 2664 Planarity : 0.004 0.037 2565 Dihedral : 8.340 71.748 3864 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.17 % Allowed : 10.22 % Favored : 86.60 % 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: 0.76 (0.19), residues: 1731 helix: 1.26 (0.25), residues: 471 sheet: 0.85 (0.22), residues: 486 loop : -0.10 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 479 HIS 0.003 0.001 HIS C 330 PHE 0.012 0.002 PHE C 376 TYR 0.015 0.002 TYR A 217 ARG 0.005 0.000 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6690 (ttm) REVERT: A 100 MET cc_start: 0.7924 (mtp) cc_final: 0.7650 (mtp) REVERT: A 167 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7553 (t0) REVERT: B 615 SER cc_start: 0.8585 (t) cc_final: 0.8353 (m) REVERT: B 632 ASP cc_start: 0.7940 (t0) cc_final: 0.7676 (t0) REVERT: C 95 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6576 (ttm) REVERT: C 161 MET cc_start: 0.8866 (tpp) cc_final: 0.8496 (tpt) REVERT: C 342 LEU cc_start: 0.9210 (tp) cc_final: 0.8941 (mt) REVERT: D 564 HIS cc_start: 0.4726 (t-90) cc_final: 0.4223 (t-90) REVERT: D 577 GLN cc_start: 0.8377 (tp-100) cc_final: 0.8143 (tt0) REVERT: D 615 SER cc_start: 0.8529 (t) cc_final: 0.8274 (m) REVERT: D 616 ASN cc_start: 0.8206 (p0) cc_final: 0.7914 (p0) REVERT: E 95 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6702 (ttm) REVERT: F 577 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7933 (tt0) REVERT: F 615 SER cc_start: 0.8666 (t) cc_final: 0.8298 (m) REVERT: F 616 ASN cc_start: 0.8413 (p0) cc_final: 0.8140 (p0) outliers start: 50 outliers final: 36 residues processed: 233 average time/residue: 0.2326 time to fit residues: 84.4947 Evaluate side-chains 211 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 414 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 6.9990 chunk 119 optimal weight: 40.0000 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15540 Z= 0.374 Angle : 0.668 9.073 21102 Z= 0.334 Chirality : 0.047 0.231 2664 Planarity : 0.004 0.039 2565 Dihedral : 7.712 60.380 3864 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.81 % Allowed : 10.60 % Favored : 85.59 % 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: 0.36 (0.19), residues: 1731 helix: 0.89 (0.24), residues: 498 sheet: 0.56 (0.22), residues: 492 loop : -0.32 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 571 HIS 0.007 0.001 HIS A 105 PHE 0.017 0.002 PHE C 376 TYR 0.019 0.002 TYR A 217 ARG 0.005 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 195 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7181 (ttm) REVERT: A 100 MET cc_start: 0.7920 (mtp) cc_final: 0.7668 (mtp) REVERT: A 161 MET cc_start: 0.9079 (tpp) cc_final: 0.8857 (tpp) REVERT: B 543 ASN cc_start: 0.8930 (t0) cc_final: 0.8624 (t0) REVERT: B 577 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7815 (mt0) REVERT: B 626 MET cc_start: 0.8004 (ttt) cc_final: 0.7668 (ttt) REVERT: B 632 ASP cc_start: 0.7981 (t0) cc_final: 0.7701 (t0) REVERT: C 95 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6841 (ttm) REVERT: C 161 MET cc_start: 0.8891 (tpp) cc_final: 0.8515 (tpt) REVERT: C 342 LEU cc_start: 0.9229 (tp) cc_final: 0.8968 (mt) REVERT: D 530 MET cc_start: 0.8920 (mmm) cc_final: 0.8516 (mtp) REVERT: D 577 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8188 (tt0) REVERT: D 615 SER cc_start: 0.8605 (t) cc_final: 0.8341 (m) REVERT: D 616 ASN cc_start: 0.8181 (p0) cc_final: 0.7868 (p0) REVERT: D 617 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7647 (ttp80) REVERT: D 626 MET cc_start: 0.7799 (ttm) cc_final: 0.7239 (ttm) REVERT: E 95 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7202 (ttm) REVERT: F 615 SER cc_start: 0.8725 (t) cc_final: 0.8393 (m) REVERT: F 616 ASN cc_start: 0.8477 (p0) cc_final: 0.8145 (p0) outliers start: 60 outliers final: 45 residues processed: 234 average time/residue: 0.2214 time to fit residues: 82.0304 Evaluate side-chains 219 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 170 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15540 Z= 0.199 Angle : 0.564 9.165 21102 Z= 0.281 Chirality : 0.045 0.237 2664 Planarity : 0.003 0.036 2565 Dihedral : 7.076 53.319 3864 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.94 % Allowed : 11.43 % Favored : 84.63 % 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: 0.41 (0.19), residues: 1731 helix: 1.18 (0.25), residues: 486 sheet: 0.64 (0.22), residues: 480 loop : -0.49 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.003 0.001 HIS A 105 PHE 0.011 0.001 PHE C 376 TYR 0.009 0.001 TYR A 217 ARG 0.003 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 188 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7006 (ttm) REVERT: A 100 MET cc_start: 0.7805 (mtp) cc_final: 0.7571 (mtp) REVERT: B 523 LEU cc_start: 0.9423 (mt) cc_final: 0.9144 (mt) REVERT: B 543 ASN cc_start: 0.9011 (t0) cc_final: 0.8671 (t0) REVERT: B 574 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7634 (mmtp) REVERT: B 626 MET cc_start: 0.8008 (ttt) cc_final: 0.7659 (ttt) REVERT: B 632 ASP cc_start: 0.7877 (t0) cc_final: 0.7578 (t0) REVERT: B 653 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 95 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6765 (ttm) REVERT: C 161 MET cc_start: 0.8881 (tpp) cc_final: 0.8553 (tpt) REVERT: C 342 LEU cc_start: 0.9079 (tp) cc_final: 0.8854 (mt) REVERT: D 530 MET cc_start: 0.8880 (mmm) cc_final: 0.8358 (mtp) REVERT: D 577 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8135 (tt0) REVERT: D 615 SER cc_start: 0.8495 (t) cc_final: 0.8244 (m) REVERT: D 616 ASN cc_start: 0.8198 (p0) cc_final: 0.7828 (p0) REVERT: E 95 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7029 (ttm) REVERT: E 195 ASN cc_start: 0.8442 (p0) cc_final: 0.8213 (p0) REVERT: E 342 LEU cc_start: 0.9074 (tp) cc_final: 0.8822 (mt) REVERT: E 426 MET cc_start: 0.6859 (ttp) cc_final: 0.6391 (ptm) REVERT: F 577 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7866 (tt0) REVERT: F 615 SER cc_start: 0.8703 (t) cc_final: 0.8404 (m) REVERT: F 616 ASN cc_start: 0.8441 (p0) cc_final: 0.8062 (p0) outliers start: 62 outliers final: 48 residues processed: 229 average time/residue: 0.2473 time to fit residues: 90.9945 Evaluate side-chains 221 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 170 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15540 Z= 0.394 Angle : 0.659 11.084 21102 Z= 0.327 Chirality : 0.047 0.252 2664 Planarity : 0.004 0.038 2565 Dihedral : 7.027 58.090 3864 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.06 % Allowed : 12.06 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1731 helix: 0.95 (0.24), residues: 498 sheet: 0.38 (0.22), residues: 474 loop : -0.58 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 571 HIS 0.007 0.001 HIS C 105 PHE 0.017 0.002 PHE C 376 TYR 0.017 0.002 TYR A 217 ARG 0.004 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 178 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7265 (ttm) REVERT: A 100 MET cc_start: 0.7936 (mtp) cc_final: 0.7628 (mtp) REVERT: B 577 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8103 (tt0) REVERT: B 626 MET cc_start: 0.8025 (ttt) cc_final: 0.7596 (ttt) REVERT: B 632 ASP cc_start: 0.7985 (t0) cc_final: 0.7757 (t0) REVERT: B 653 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 95 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6912 (ttm) REVERT: C 150 MET cc_start: 0.8981 (mtp) cc_final: 0.8663 (mmm) REVERT: C 161 MET cc_start: 0.8923 (tpp) cc_final: 0.8531 (tpt) REVERT: C 342 LEU cc_start: 0.9175 (tp) cc_final: 0.8930 (mt) REVERT: D 530 MET cc_start: 0.8930 (mmm) cc_final: 0.8334 (mtp) REVERT: D 577 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8154 (tt0) REVERT: D 615 SER cc_start: 0.8460 (t) cc_final: 0.8230 (m) REVERT: D 616 ASN cc_start: 0.8238 (p0) cc_final: 0.7855 (p0) REVERT: E 95 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7340 (ttm) REVERT: E 342 LEU cc_start: 0.9163 (tp) cc_final: 0.8908 (mt) REVERT: F 542 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7588 (ptm160) REVERT: F 577 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7831 (tt0) REVERT: F 615 SER cc_start: 0.8726 (t) cc_final: 0.8449 (m) REVERT: F 616 ASN cc_start: 0.8435 (p0) cc_final: 0.7992 (p0) outliers start: 64 outliers final: 54 residues processed: 221 average time/residue: 0.2225 time to fit residues: 78.4003 Evaluate side-chains 217 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 160 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15540 Z= 0.190 Angle : 0.557 9.199 21102 Z= 0.277 Chirality : 0.045 0.250 2664 Planarity : 0.003 0.034 2565 Dihedral : 6.289 53.548 3864 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.05 % Allowed : 13.84 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1731 helix: 1.12 (0.25), residues: 486 sheet: 0.37 (0.22), residues: 474 loop : -0.57 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.003 0.001 HIS C 105 PHE 0.010 0.001 PHE E 376 TYR 0.008 0.001 TYR A 191 ARG 0.004 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7019 (ttm) REVERT: A 100 MET cc_start: 0.7818 (mtp) cc_final: 0.7570 (mtp) REVERT: B 523 LEU cc_start: 0.9409 (mt) cc_final: 0.9154 (mt) REVERT: B 617 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7422 (ttp80) REVERT: B 653 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 95 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6791 (ttm) REVERT: C 150 MET cc_start: 0.8994 (mtp) cc_final: 0.8661 (mmm) REVERT: C 161 MET cc_start: 0.8908 (tpp) cc_final: 0.8558 (tpt) REVERT: C 342 LEU cc_start: 0.9078 (tp) cc_final: 0.8874 (mt) REVERT: C 426 MET cc_start: 0.6875 (ttp) cc_final: 0.6499 (ptm) REVERT: D 523 LEU cc_start: 0.9396 (mt) cc_final: 0.9090 (mt) REVERT: D 530 MET cc_start: 0.8899 (mmm) cc_final: 0.8436 (mtp) REVERT: D 615 SER cc_start: 0.8366 (t) cc_final: 0.8137 (m) REVERT: D 616 ASN cc_start: 0.8113 (p0) cc_final: 0.7701 (p0) REVERT: D 653 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7300 (tm-30) REVERT: E 95 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7050 (ttm) REVERT: E 195 ASN cc_start: 0.8417 (p0) cc_final: 0.8207 (p0) REVERT: E 342 LEU cc_start: 0.9035 (tp) cc_final: 0.8795 (mt) REVERT: F 523 LEU cc_start: 0.9422 (mt) cc_final: 0.9065 (mt) REVERT: F 530 MET cc_start: 0.8772 (mmm) cc_final: 0.8324 (mtp) REVERT: F 542 ARG cc_start: 0.7822 (ptm160) cc_final: 0.7512 (ptm160) REVERT: F 577 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7892 (tt0) REVERT: F 615 SER cc_start: 0.8705 (t) cc_final: 0.8415 (m) REVERT: F 616 ASN cc_start: 0.8383 (p0) cc_final: 0.7937 (p0) REVERT: F 626 MET cc_start: 0.7492 (ttt) cc_final: 0.7123 (ttt) outliers start: 48 outliers final: 41 residues processed: 217 average time/residue: 0.2163 time to fit residues: 75.1314 Evaluate side-chains 215 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 171 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 658 GLN D 577 GLN E 170 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15540 Z= 0.160 Angle : 0.536 12.643 21102 Z= 0.266 Chirality : 0.044 0.248 2664 Planarity : 0.003 0.033 2565 Dihedral : 5.676 54.240 3864 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.75 % Allowed : 13.84 % Favored : 82.41 % 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: 0.53 (0.20), residues: 1731 helix: 1.55 (0.25), residues: 459 sheet: 0.34 (0.21), residues: 504 loop : -0.29 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 571 HIS 0.002 0.001 HIS A 374 PHE 0.009 0.001 PHE C 376 TYR 0.007 0.001 TYR A 191 ARG 0.002 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 186 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7779 (mtp) cc_final: 0.7570 (mtp) REVERT: A 161 MET cc_start: 0.8955 (tpp) cc_final: 0.8372 (tpp) REVERT: B 523 LEU cc_start: 0.9391 (mt) cc_final: 0.9124 (mt) REVERT: B 535 MET cc_start: 0.8007 (mmp) cc_final: 0.7805 (mmp) REVERT: B 653 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7744 (tm-30) REVERT: C 95 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6736 (ttm) REVERT: C 150 MET cc_start: 0.8974 (mtp) cc_final: 0.8603 (mmm) REVERT: C 161 MET cc_start: 0.8918 (tpp) cc_final: 0.8589 (tpt) REVERT: C 342 LEU cc_start: 0.9015 (tp) cc_final: 0.8669 (tp) REVERT: C 390 LEU cc_start: 0.9007 (mt) cc_final: 0.8719 (mt) REVERT: C 468 PHE cc_start: 0.8843 (m-80) cc_final: 0.8630 (m-80) REVERT: D 523 LEU cc_start: 0.9348 (mt) cc_final: 0.9060 (mt) REVERT: D 530 MET cc_start: 0.8893 (mmm) cc_final: 0.8223 (mtp) REVERT: D 577 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: D 616 ASN cc_start: 0.8113 (p0) cc_final: 0.7885 (p0) REVERT: D 653 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7507 (tm-30) REVERT: E 95 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6742 (ttm) REVERT: E 195 ASN cc_start: 0.8368 (p0) cc_final: 0.8164 (p0) REVERT: E 342 LEU cc_start: 0.8969 (tp) cc_final: 0.8575 (tp) REVERT: F 523 LEU cc_start: 0.9384 (mt) cc_final: 0.9044 (mt) REVERT: F 542 ARG cc_start: 0.7857 (ptm160) cc_final: 0.7547 (ptm160) REVERT: F 577 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8000 (tt0) REVERT: F 615 SER cc_start: 0.8704 (t) cc_final: 0.8415 (m) REVERT: F 616 ASN cc_start: 0.8348 (p0) cc_final: 0.7872 (p0) outliers start: 59 outliers final: 46 residues processed: 227 average time/residue: 0.2182 time to fit residues: 79.6417 Evaluate side-chains 218 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 169 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 0.0370 chunk 141 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN D 577 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15540 Z= 0.191 Angle : 0.551 11.286 21102 Z= 0.274 Chirality : 0.044 0.253 2664 Planarity : 0.003 0.032 2565 Dihedral : 5.798 57.441 3864 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.56 % Allowed : 13.97 % Favored : 82.48 % 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: 0.49 (0.20), residues: 1731 helix: 1.48 (0.25), residues: 468 sheet: 0.33 (0.21), residues: 504 loop : -0.32 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 96 HIS 0.003 0.001 HIS C 105 PHE 0.011 0.001 PHE C 376 TYR 0.027 0.001 TYR E 191 ARG 0.003 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 182 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7801 (mtp) cc_final: 0.7594 (mtp) REVERT: B 523 LEU cc_start: 0.9412 (mt) cc_final: 0.9143 (mt) REVERT: B 535 MET cc_start: 0.8030 (mmp) cc_final: 0.7806 (mmp) REVERT: B 617 ARG cc_start: 0.7456 (tpp80) cc_final: 0.7158 (tpp80) REVERT: B 653 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 150 MET cc_start: 0.8975 (mtp) cc_final: 0.8627 (mmm) REVERT: C 161 MET cc_start: 0.8930 (tpp) cc_final: 0.8594 (tpt) REVERT: C 342 LEU cc_start: 0.9026 (tp) cc_final: 0.8689 (tp) REVERT: C 390 LEU cc_start: 0.9060 (mt) cc_final: 0.8816 (mt) REVERT: C 468 PHE cc_start: 0.8837 (m-80) cc_final: 0.8610 (m-80) REVERT: D 523 LEU cc_start: 0.9359 (mt) cc_final: 0.9060 (mt) REVERT: D 530 MET cc_start: 0.8899 (mmm) cc_final: 0.8178 (mtp) REVERT: D 577 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: D 632 ASP cc_start: 0.7826 (t0) cc_final: 0.7615 (t0) REVERT: D 653 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7532 (tm-30) REVERT: E 195 ASN cc_start: 0.8378 (p0) cc_final: 0.8155 (p0) REVERT: E 342 LEU cc_start: 0.8979 (tp) cc_final: 0.8637 (tp) REVERT: F 523 LEU cc_start: 0.9401 (mt) cc_final: 0.9057 (mt) REVERT: F 542 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7496 (ptm160) REVERT: F 577 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7966 (tt0) REVERT: F 615 SER cc_start: 0.8699 (t) cc_final: 0.8412 (m) REVERT: F 616 ASN cc_start: 0.8392 (p0) cc_final: 0.7899 (p0) outliers start: 56 outliers final: 50 residues processed: 221 average time/residue: 0.2220 time to fit residues: 77.4901 Evaluate side-chains 224 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 173 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN D 577 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15540 Z= 0.177 Angle : 0.551 16.138 21102 Z= 0.274 Chirality : 0.045 0.319 2664 Planarity : 0.003 0.032 2565 Dihedral : 5.691 54.309 3864 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.30 % Allowed : 14.29 % Favored : 82.41 % 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: 0.49 (0.20), residues: 1731 helix: 1.46 (0.25), residues: 468 sheet: 0.35 (0.21), residues: 504 loop : -0.31 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 571 HIS 0.003 0.001 HIS C 105 PHE 0.010 0.001 PHE E 376 TYR 0.026 0.001 TYR A 191 ARG 0.002 0.000 ARG C 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 180 time to evaluate : 1.799 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: A 100 MET cc_start: 0.7793 (mtp) cc_final: 0.7585 (mtp) REVERT: B 523 LEU cc_start: 0.9409 (mt) cc_final: 0.9143 (mt) REVERT: B 535 MET cc_start: 0.7989 (mmp) cc_final: 0.7782 (mmp) REVERT: B 653 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 150 MET cc_start: 0.8973 (mtp) cc_final: 0.8633 (mmm) REVERT: C 161 MET cc_start: 0.8929 (tpp) cc_final: 0.8603 (tpt) REVERT: C 342 LEU cc_start: 0.9007 (tp) cc_final: 0.8714 (tp) REVERT: C 390 LEU cc_start: 0.9088 (mt) cc_final: 0.8853 (mt) REVERT: C 468 PHE cc_start: 0.8826 (m-80) cc_final: 0.8604 (m-80) REVERT: D 523 LEU cc_start: 0.9351 (mt) cc_final: 0.9061 (mt) REVERT: D 530 MET cc_start: 0.8923 (mmm) cc_final: 0.8167 (mtp) REVERT: D 577 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: D 653 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 95 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6906 (ttm) REVERT: E 195 ASN cc_start: 0.8421 (p0) cc_final: 0.8170 (p0) REVERT: E 342 LEU cc_start: 0.8975 (tp) cc_final: 0.8642 (tp) REVERT: E 434 MET cc_start: 0.8468 (ttp) cc_final: 0.8198 (ttp) REVERT: F 523 LEU cc_start: 0.9394 (mt) cc_final: 0.9061 (mt) REVERT: F 542 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7484 (ptm160) REVERT: F 577 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8033 (tt0) REVERT: F 615 SER cc_start: 0.8678 (t) cc_final: 0.8404 (m) REVERT: F 616 ASN cc_start: 0.8382 (p0) cc_final: 0.7882 (p0) outliers start: 52 outliers final: 47 residues processed: 217 average time/residue: 0.2284 time to fit residues: 78.3609 Evaluate side-chains 223 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 138 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103421 restraints weight = 22635.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106209 restraints weight = 15853.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108148 restraints weight = 12562.275| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 15540 Z= 0.249 Angle : 0.816 59.188 21102 Z= 0.453 Chirality : 0.045 0.357 2664 Planarity : 0.004 0.144 2565 Dihedral : 5.711 54.310 3864 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.24 % Allowed : 14.41 % Favored : 82.35 % Cbeta Deviations : 0.06 % 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: 0.47 (0.20), residues: 1731 helix: 1.41 (0.25), residues: 468 sheet: 0.35 (0.21), residues: 504 loop : -0.32 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 631 HIS 0.003 0.001 HIS C 105 PHE 0.011 0.001 PHE E 376 TYR 0.023 0.001 TYR A 191 ARG 0.002 0.000 ARG B 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.13 seconds wall clock time: 52 minutes 53.32 seconds (3173.32 seconds total)