Starting phenix.real_space_refine on Thu Jul 25 00:28:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b39_44132/07_2024/9b39_44132.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b39_44132/07_2024/9b39_44132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b39_44132/07_2024/9b39_44132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b39_44132/07_2024/9b39_44132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b39_44132/07_2024/9b39_44132.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b39_44132/07_2024/9b39_44132.cif" } resolution = 3.84 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= 0.019 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 160 5.16 5 C 17571 2.51 5 N 4512 2.21 5 O 5279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 748": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 748": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 866": "NH1" <-> "NH2" Residue "B ARG 873": "NH1" <-> "NH2" Residue "B ARG 874": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 748": "NH1" <-> "NH2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 866": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D ARG 663": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Residue "D ARG 866": "NH1" <-> "NH2" Residue "D ARG 873": "NH1" <-> "NH2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "B GLU 1001": "OE1" <-> "OE2" Residue "C GLU 1001": "OE1" <-> "OE2" Residue "D GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27522 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6684 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6818 Chain: "B" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "C" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "D" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 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: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 25.74, per 1000 atoms: 0.94 Number of scatterers: 27522 At special positions: 0 Unit cell: (157.798, 126.778, 205.002, 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 160 16.00 O 5279 8.00 N 4512 7.00 C 17571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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 E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " 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 J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A1002 " - " ASN A 67 " " NAG A1003 " - " ASN A 73 " " NAG A1004 " - " ASN A 423 " " NAG A1005 " - " ASN A 751 " " NAG B1002 " - " ASN B 67 " " NAG B1003 " - " ASN B 73 " " NAG B1004 " - " ASN B 378 " " NAG B1005 " - " ASN B 412 " " NAG B1006 " - " ASN B 546 " " NAG C1002 " - " ASN C 67 " " NAG C1003 " - " ASN C 73 " " NAG C1004 " - " ASN C 412 " " NAG C1005 " - " ASN C 423 " " NAG C1006 " - " ASN C 546 " " NAG C1007 " - " ASN C 751 " " NAG D1002 " - " ASN D 67 " " NAG D1003 " - " ASN D 73 " " NAG D1004 " - " ASN D 430 " " NAG D1005 " - " ASN D 546 " " NAG D1006 " - " ASN D 751 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 412 " " NAG H 1 " - " ASN A 430 " " NAG I 1 " - " ASN B 275 " " NAG J 1 " - " ASN C 275 " " NAG K 1 " - " ASN C 378 " " NAG L 1 " - " ASN C 430 " " NAG M 1 " - " ASN D 378 " " NAG N 1 " - " ASN D 412 " Time building additional restraints: 12.01 Conformation dependent library (CDL) restraints added in 10.3 seconds 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6306 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 32 sheets defined 45.7% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 51 through 66 removed outlier: 3.514A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.554A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.583A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.527A pdb=" N SER A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.995A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.122A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.735A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.016A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.579A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.685A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 500 through 507 removed outlier: 4.001A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.670A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.550A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 4.032A pdb=" N PHE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 664 removed outlier: 3.686A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.525A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.634A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.584A pdb=" N VAL A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.658A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.718A pdb=" N ARG A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 788 Processing helix chain 'A' and resid 789 through 798 removed outlier: 4.280A pdb=" N GLU A 796 " --> pdb=" O HIS A 792 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 851 removed outlier: 3.664A pdb=" N GLY A 830 " --> pdb=" O VAL A 826 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 864 removed outlier: 3.781A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 864 " --> pdb=" O ALA A 860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 859 through 864' Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.605A pdb=" N ALA B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.500A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.536A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.179A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.537A pdb=" N ARG B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.663A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.835A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 286 through 300 removed outlier: 3.615A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.687A pdb=" N SER B 309 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 310' Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.564A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 4.343A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.858A pdb=" N ARG B 458 " --> pdb=" O GLY B 455 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 459 " --> pdb=" O ASN B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 459' Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.591A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.511A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.950A pdb=" N VAL B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 661 removed outlier: 3.526A pdb=" N TRP B 640 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 removed outlier: 3.689A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 710 removed outlier: 3.933A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 710 " --> pdb=" O TRP B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.534A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 728 " --> pdb=" O GLY B 724 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 729 " --> pdb=" O ILE B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.632A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 789 removed outlier: 3.551A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 4.036A pdb=" N LYS B 797 " --> pdb=" O MET B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 853 removed outlier: 3.680A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 831 " --> pdb=" O LEU B 827 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 836 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 852 " --> pdb=" O LYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 868 removed outlier: 3.952A pdb=" N GLU B 864 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 865 " --> pdb=" O MET B 861 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.720A pdb=" N ASN C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.841A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.609A pdb=" N SER C 157 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.739A pdb=" N LEU C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.560A pdb=" N ARG C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.719A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 317 through 337 removed outlier: 4.033A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 4.412A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 560 through 582 removed outlier: 3.505A pdb=" N VAL C 574 " --> pdb=" O ALA C 570 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.603A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.817A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 688 through 694 Processing helix chain 'C' and resid 699 through 712 Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.508A pdb=" N GLY C 724 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 749 removed outlier: 3.639A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.953A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 798 removed outlier: 3.746A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 822 through 853 removed outlier: 4.134A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 853 " --> pdb=" O ASN C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 870 removed outlier: 4.006A pdb=" N VAL C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 863 " --> pdb=" O SER C 859 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C 866 " --> pdb=" O VAL C 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.852A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 168 removed outlier: 3.561A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.616A pdb=" N LEU D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.622A pdb=" N LYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.501A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.618A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 removed outlier: 3.812A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.714A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.868A pdb=" N GLN D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 491 through 495 removed outlier: 3.679A pdb=" N ASN D 495 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.705A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 4.135A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.585A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 579 " --> pdb=" O SER D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.536A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY D 615 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY D 617 " --> pdb=" O TRP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 665 removed outlier: 3.502A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG D 663 " --> pdb=" O LEU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 676 removed outlier: 3.519A pdb=" N LYS D 676 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 713 removed outlier: 3.564A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER D 710 " --> pdb=" O TRP D 706 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG D 713 " --> pdb=" O MET D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 730 removed outlier: 3.747A pdb=" N LEU D 729 " --> pdb=" O ILE D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 749 removed outlier: 3.559A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 745 " --> pdb=" O THR D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 789 removed outlier: 3.560A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.561A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 821 removed outlier: 3.841A pdb=" N ILE D 820 " --> pdb=" O GLY D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 839 removed outlier: 3.631A pdb=" N VAL D 839 " --> pdb=" O VAL D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 853 Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.121A pdb=" N VAL D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 863 " --> pdb=" O SER D 859 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 865 " --> pdb=" O MET D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 874 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.783A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 253 through 255 removed outlier: 6.731A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 removed outlier: 5.769A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 535 removed outlier: 3.560A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.601A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 83 removed outlier: 7.296A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 39 " --> pdb=" O ALA B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.532A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB4, first strand: chain 'B' and resid 389 through 395 removed outlier: 4.005A pdb=" N GLY B 403 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER B 393 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS B 401 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS B 395 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AB6, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.505A pdb=" N LYS B 762 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 682 through 683 removed outlier: 3.835A pdb=" N PHE B 735 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB9, first strand: chain 'C' and resid 129 through 131 removed outlier: 7.035A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.466A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 280 removed outlier: 6.815A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 432 through 435 Processing sheet with id=AC4, first strand: chain 'C' and resid 513 through 517 removed outlier: 7.902A pdb=" N ALA C 515 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLY C 767 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 517 " --> pdb=" O GLY C 765 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AC6, first strand: chain 'D' and resid 34 through 35 removed outlier: 5.756A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.709A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 129 through 131 removed outlier: 4.033A pdb=" N GLY D 382 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.658A pdb=" N TYR D 176 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 225 through 226 Processing sheet with id=AD2, first strand: chain 'D' and resid 392 through 395 removed outlier: 3.720A pdb=" N GLU D 400 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD4, first strand: chain 'D' and resid 517 through 518 removed outlier: 4.566A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 764 " --> pdb=" O MET D 534 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 540 through 542 removed outlier: 4.100A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2756 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: 8.40 Time building geometry restraints manager: 12.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8225 1.34 - 1.46: 6884 1.46 - 1.58: 12738 1.58 - 1.71: 4 1.71 - 1.83: 272 Bond restraints: 28123 Sorted by residual: bond pdb=" C ALA D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.336 1.405 -0.069 1.08e-02 8.57e+03 4.10e+01 bond pdb=" C ALA B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.336 1.401 -0.065 1.08e-02 8.57e+03 3.65e+01 bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.511 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CA HIS A 136 " pdb=" CB HIS A 136 " ideal model delta sigma weight residual 1.527 1.461 0.067 1.30e-02 5.92e+03 2.62e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 28118 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.90: 678 105.90 - 114.32: 16346 114.32 - 122.74: 18114 122.74 - 131.16: 2804 131.16 - 139.58: 129 Bond angle restraints: 38071 Sorted by residual: angle pdb=" C GLU C 441 " pdb=" N PRO C 442 " pdb=" CA PRO C 442 " ideal model delta sigma weight residual 119.84 131.79 -11.95 1.25e+00 6.40e-01 9.14e+01 angle pdb=" C VAL C 274 " pdb=" N ASN C 275 " pdb=" CA ASN C 275 " ideal model delta sigma weight residual 122.41 111.14 11.27 1.41e+00 5.03e-01 6.38e+01 angle pdb=" C ARG A 374 " pdb=" N ILE A 375 " pdb=" CA ILE A 375 " ideal model delta sigma weight residual 121.97 136.29 -14.32 1.80e+00 3.09e-01 6.33e+01 angle pdb=" N VAL C 274 " pdb=" CA VAL C 274 " pdb=" C VAL C 274 " ideal model delta sigma weight residual 108.06 98.95 9.11 1.28e+00 6.10e-01 5.06e+01 angle pdb=" N ILE D 281 " pdb=" CA ILE D 281 " pdb=" C ILE D 281 " ideal model delta sigma weight residual 113.10 106.20 6.90 9.70e-01 1.06e+00 5.05e+01 ... (remaining 38066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 16704 25.61 - 51.23: 611 51.23 - 76.84: 108 76.84 - 102.46: 90 102.46 - 128.07: 82 Dihedral angle restraints: 17595 sinusoidal: 7795 harmonic: 9800 Sorted by residual: dihedral pdb=" CA GLU C 441 " pdb=" C GLU C 441 " pdb=" N PRO C 442 " pdb=" CA PRO C 442 " ideal model delta harmonic sigma weight residual -180.00 -111.51 -68.49 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" CA CYS D 804 " pdb=" C CYS D 804 " pdb=" N PRO D 805 " pdb=" CA PRO D 805 " ideal model delta harmonic sigma weight residual 180.00 119.70 60.30 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA PRO B 72 " pdb=" C PRO B 72 " pdb=" N ASN B 73 " pdb=" CA ASN B 73 " ideal model delta harmonic sigma weight residual -180.00 -123.31 -56.69 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 17592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4338 0.197 - 0.394: 64 0.394 - 0.591: 8 0.591 - 0.788: 1 0.788 - 0.985: 1 Chirality restraints: 4412 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 430 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" C1 NAG D1004 " pdb=" ND2 ASN D 430 " pdb=" C2 NAG D1004 " pdb=" O5 NAG D1004 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG B1006 " pdb=" ND2 ASN B 546 " pdb=" C2 NAG B1006 " pdb=" O5 NAG B1006 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.54e+00 ... (remaining 4409 not shown) Planarity restraints: 4783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1002 " -0.292 2.00e-02 2.50e+03 2.47e-01 7.66e+02 pdb=" C7 NAG A1002 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1002 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A1002 " 0.426 2.00e-02 2.50e+03 pdb=" O7 NAG A1002 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1004 " 0.123 2.00e-02 2.50e+03 1.00e-01 1.26e+02 pdb=" C7 NAG B1004 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG B1004 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG B1004 " -0.157 2.00e-02 2.50e+03 pdb=" O7 NAG B1004 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS D 804 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO D 805 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO D 805 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 805 " 0.063 5.00e-02 4.00e+02 ... (remaining 4780 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2456 2.73 - 3.27: 27886 3.27 - 3.81: 46112 3.81 - 4.36: 55049 4.36 - 4.90: 88381 Nonbonded interactions: 219884 Sorted by model distance: nonbonded pdb=" O ASP D 528 " pdb=" OG1 THR D 768 " model vdw 2.184 2.440 nonbonded pdb=" OE2 GLU A 250 " pdb=" OH TYR A 774 " model vdw 2.236 2.440 nonbonded pdb=" OE1 GLU D 738 " pdb=" OH TYR D 764 " model vdw 2.237 2.440 nonbonded pdb=" O LYS D 629 " pdb=" OG1 THR D 633 " model vdw 2.262 2.440 nonbonded pdb=" O PHE D 693 " pdb=" OG SER D 697 " model vdw 2.262 2.440 ... (remaining 219879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874 or resid 1001 or resid 1002 through 1005)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874 or resid 1001 or resid 1002 through 1005)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874 or resid 1001 or resid 1002 through 1005)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874 or resid 1001 or resid 1002 through 1005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 87.780 Find NCS groups from input model: 3.270 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.009 0.105 28123 Z= 0.565 Angle : 1.535 23.276 38071 Z= 0.860 Chirality : 0.073 0.985 4412 Planarity : 0.009 0.247 4753 Dihedral : 17.939 128.074 11265 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 1.46 % Allowed : 15.33 % Favored : 83.21 % Rotamer: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.33 % 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: -5.60 (0.11), residues: 3365 helix: -3.43 (0.09), residues: 1382 sheet: -4.66 (0.20), residues: 330 loop : -3.77 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP B 589 HIS 0.038 0.004 HIS D 253 PHE 0.049 0.004 PHE A 167 TYR 0.051 0.004 TYR D 195 ARG 0.021 0.001 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 457 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 LEU cc_start: 0.9210 (mp) cc_final: 0.8862 (mt) REVERT: A 454 TYR cc_start: 0.8767 (m-80) cc_final: 0.8296 (m-80) REVERT: A 517 LEU cc_start: 0.9088 (mm) cc_final: 0.8624 (mm) REVERT: A 578 LEU cc_start: 0.9356 (tt) cc_final: 0.9125 (pp) REVERT: A 665 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7550 (pp20) REVERT: A 824 PHE cc_start: 0.8673 (m-80) cc_final: 0.8097 (m-80) REVERT: A 867 MET cc_start: 0.7130 (tpt) cc_final: 0.6881 (tpp) REVERT: B 248 MET cc_start: 0.8212 (mmm) cc_final: 0.8005 (mmm) REVERT: B 608 LEU cc_start: 0.8909 (mp) cc_final: 0.8407 (mm) REVERT: B 612 PHE cc_start: 0.8305 (m-10) cc_final: 0.8066 (m-80) REVERT: B 639 ILE cc_start: 0.8987 (mm) cc_final: 0.8712 (pt) REVERT: B 694 PHE cc_start: 0.8360 (m-80) cc_final: 0.7721 (m-80) REVERT: B 719 LYS cc_start: 0.8853 (mttp) cc_final: 0.7771 (tppt) REVERT: B 784 GLN cc_start: 0.8905 (tt0) cc_final: 0.8568 (mt0) REVERT: B 810 LYS cc_start: 0.7423 (mttp) cc_final: 0.6495 (pttt) REVERT: B 815 LEU cc_start: 0.8638 (tp) cc_final: 0.8424 (tp) REVERT: B 842 PHE cc_start: 0.7530 (t80) cc_final: 0.6550 (t80) REVERT: C 360 MET cc_start: 0.9383 (tpt) cc_final: 0.8757 (tpt) REVERT: C 448 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7750 (tptp) REVERT: C 454 TYR cc_start: 0.8302 (m-80) cc_final: 0.8005 (m-80) REVERT: C 501 MET cc_start: 0.8502 (mpt) cc_final: 0.8231 (mmm) REVERT: C 503 ARG cc_start: 0.9078 (ttt180) cc_final: 0.8838 (mmm-85) REVERT: C 556 LEU cc_start: 0.9014 (mp) cc_final: 0.8771 (tt) REVERT: C 584 PHE cc_start: 0.7537 (m-10) cc_final: 0.7207 (m-80) REVERT: C 627 MET cc_start: 0.7406 (mmp) cc_final: 0.6961 (mmp) REVERT: C 651 TYR cc_start: 0.9149 (t80) cc_final: 0.8768 (t80) REVERT: C 673 ASP cc_start: 0.8820 (m-30) cc_final: 0.8548 (m-30) REVERT: C 686 GLU cc_start: 0.8778 (tt0) cc_final: 0.8428 (tp30) REVERT: C 691 MET cc_start: 0.8542 (tmt) cc_final: 0.8172 (tmm) REVERT: C 705 MET cc_start: 0.9190 (mtp) cc_final: 0.8908 (mtp) REVERT: C 723 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8047 (tp30) REVERT: C 764 TYR cc_start: 0.6979 (m-10) cc_final: 0.6631 (m-80) REVERT: C 815 LEU cc_start: 0.8704 (mt) cc_final: 0.8433 (mt) REVERT: D 114 SER cc_start: 0.9411 (m) cc_final: 0.9201 (t) REVERT: D 248 MET cc_start: 0.8773 (mmm) cc_final: 0.8558 (mmm) REVERT: D 566 TYR cc_start: 0.8474 (m-10) cc_final: 0.8107 (t80) REVERT: D 571 CYS cc_start: 0.8299 (t) cc_final: 0.8075 (p) REVERT: D 584 PHE cc_start: 0.8488 (t80) cc_final: 0.7997 (t80) REVERT: D 590 TYR cc_start: 0.8390 (p90) cc_final: 0.8151 (p90) REVERT: D 626 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7914 (tt) REVERT: D 662 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8812 (mm-30) REVERT: D 861 MET cc_start: 0.6402 (mtt) cc_final: 0.5872 (mmm) outliers start: 9 outliers final: 1 residues processed: 462 average time/residue: 0.4032 time to fit residues: 290.9288 Evaluate side-chains 256 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 626 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 196 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 123 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS A 165 GLN A 186 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS A 605 ASN A 610 ASN A 622 GLN A 754 GLN B 34 HIS ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 593 HIS B 654 ASN B 792 HIS C 123 ASN C 136 HIS C 165 GLN C 283 ASN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN C 557 ASN C 622 GLN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 819 ASN D 65 ASN D 232 HIS D 286 ASN D 456 ASN D 604 ASN D 622 GLN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN D 784 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28123 Z= 0.286 Angle : 0.980 16.409 38071 Z= 0.483 Chirality : 0.053 0.564 4412 Planarity : 0.007 0.140 4753 Dihedral : 19.303 110.636 4840 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.79 % Favored : 84.14 % Rotamer: Outliers : 1.77 % Allowed : 11.46 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.74 % 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: -4.39 (0.12), residues: 3365 helix: -1.90 (0.11), residues: 1462 sheet: -4.43 (0.21), residues: 342 loop : -3.57 (0.14), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 589 HIS 0.011 0.001 HIS D 253 PHE 0.038 0.002 PHE B 643 TYR 0.021 0.002 TYR C 254 ARG 0.017 0.001 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 289 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9208 (tm) REVERT: A 454 TYR cc_start: 0.8842 (m-80) cc_final: 0.8631 (m-80) REVERT: A 517 LEU cc_start: 0.8971 (mm) cc_final: 0.8681 (mm) REVERT: A 562 ASP cc_start: 0.8032 (m-30) cc_final: 0.7518 (m-30) REVERT: A 565 MET cc_start: 0.8834 (ptt) cc_final: 0.8574 (ptt) REVERT: A 578 LEU cc_start: 0.9341 (tt) cc_final: 0.8969 (pp) REVERT: A 606 PHE cc_start: 0.8246 (m-80) cc_final: 0.7849 (t80) REVERT: A 612 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8296 (p90) REVERT: A 620 MET cc_start: 0.9003 (mmm) cc_final: 0.7748 (mmm) REVERT: A 768 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.7295 (p) REVERT: A 770 MET cc_start: 0.8583 (tpp) cc_final: 0.7772 (tpp) REVERT: A 824 PHE cc_start: 0.8621 (m-80) cc_final: 0.8289 (m-80) REVERT: B 719 LYS cc_start: 0.8874 (mttp) cc_final: 0.7718 (tppt) REVERT: B 762 LYS cc_start: 0.8323 (mppt) cc_final: 0.7708 (mmtt) REVERT: B 794 MET cc_start: 0.7335 (mmt) cc_final: 0.7125 (mmp) REVERT: B 842 PHE cc_start: 0.7358 (t80) cc_final: 0.7041 (t80) REVERT: C 250 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: C 413 MET cc_start: 0.7449 (ppp) cc_final: 0.7203 (ppp) REVERT: C 448 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7754 (tptp) REVERT: C 454 TYR cc_start: 0.8314 (m-80) cc_final: 0.8018 (m-80) REVERT: C 463 CYS cc_start: 0.9127 (m) cc_final: 0.8645 (m) REVERT: C 501 MET cc_start: 0.8793 (mpt) cc_final: 0.8251 (mmm) REVERT: C 503 ARG cc_start: 0.9143 (ttt180) cc_final: 0.8921 (mmm-85) REVERT: C 556 LEU cc_start: 0.9104 (mp) cc_final: 0.8743 (tt) REVERT: C 691 MET cc_start: 0.8533 (tmt) cc_final: 0.8283 (tmm) REVERT: C 764 TYR cc_start: 0.6886 (m-10) cc_final: 0.6668 (m-80) REVERT: C 794 MET cc_start: 0.8485 (ptm) cc_final: 0.7843 (ptm) REVERT: D 114 SER cc_start: 0.9437 (m) cc_final: 0.9196 (t) REVERT: D 248 MET cc_start: 0.8836 (mmm) cc_final: 0.8597 (mmm) REVERT: D 340 MET cc_start: 0.7470 (tpp) cc_final: 0.7193 (tmm) REVERT: D 360 MET cc_start: 0.8765 (tpp) cc_final: 0.8508 (tpp) REVERT: D 566 TYR cc_start: 0.7838 (m-10) cc_final: 0.7604 (m-80) REVERT: D 584 PHE cc_start: 0.8496 (t80) cc_final: 0.8057 (t80) REVERT: D 662 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8622 (tm-30) REVERT: D 691 MET cc_start: 0.8652 (tmm) cc_final: 0.8186 (tmm) REVERT: D 780 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8553 (tp) REVERT: D 793 MET cc_start: 0.8814 (tpp) cc_final: 0.8534 (ttp) REVERT: D 861 MET cc_start: 0.6326 (mtt) cc_final: 0.5994 (mmm) outliers start: 48 outliers final: 28 residues processed: 324 average time/residue: 0.3855 time to fit residues: 201.0249 Evaluate side-chains 257 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 481 ARG Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 303 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 245 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 621 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 819 ASN C 137 GLN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 593 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28123 Z= 0.380 Angle : 0.964 14.662 38071 Z= 0.472 Chirality : 0.053 0.574 4412 Planarity : 0.006 0.126 4753 Dihedral : 17.407 111.171 4838 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 1.01 % Allowed : 16.10 % Favored : 82.89 % Rotamer: Outliers : 2.62 % Allowed : 12.68 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.62 % 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: -3.66 (0.13), residues: 3365 helix: -0.98 (0.12), residues: 1445 sheet: -4.45 (0.21), residues: 339 loop : -3.41 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 589 HIS 0.020 0.002 HIS D 350 PHE 0.045 0.003 PHE C 262 TYR 0.021 0.002 TYR C 252 ARG 0.011 0.001 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 242 time to evaluate : 3.256 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 84 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8880 (t160) REVERT: A 85 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9301 (tm) REVERT: A 145 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: A 298 MET cc_start: 0.7939 (tmm) cc_final: 0.7548 (tmm) REVERT: A 316 MET cc_start: 0.8308 (mmm) cc_final: 0.7780 (tpt) REVERT: A 454 TYR cc_start: 0.8677 (m-80) cc_final: 0.8457 (m-80) REVERT: A 517 LEU cc_start: 0.9168 (mm) cc_final: 0.8745 (mm) REVERT: A 562 ASP cc_start: 0.7972 (m-30) cc_final: 0.7594 (p0) REVERT: A 565 MET cc_start: 0.8949 (ptt) cc_final: 0.8687 (ptt) REVERT: A 612 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8217 (p90) REVERT: A 691 MET cc_start: 0.8859 (ttp) cc_final: 0.8507 (ptm) REVERT: A 768 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7721 (p) REVERT: A 770 MET cc_start: 0.8606 (tpp) cc_final: 0.7582 (tpp) REVERT: A 824 PHE cc_start: 0.8612 (m-80) cc_final: 0.8255 (m-80) REVERT: B 651 TYR cc_start: 0.9060 (t80) cc_final: 0.8614 (t80) REVERT: B 719 LYS cc_start: 0.8927 (mttp) cc_final: 0.7882 (tppt) REVERT: B 762 LYS cc_start: 0.8326 (mppt) cc_final: 0.7720 (mmtt) REVERT: B 794 MET cc_start: 0.7367 (mmt) cc_final: 0.7158 (mmp) REVERT: B 842 PHE cc_start: 0.7029 (t80) cc_final: 0.6631 (t80) REVERT: C 250 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: C 339 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7385 (tp40) REVERT: C 413 MET cc_start: 0.7685 (ppp) cc_final: 0.6716 (ppp) REVERT: C 428 LEU cc_start: 0.8254 (tt) cc_final: 0.8024 (tp) REVERT: C 463 CYS cc_start: 0.9110 (m) cc_final: 0.8610 (m) REVERT: C 501 MET cc_start: 0.8815 (mpt) cc_final: 0.8252 (mmm) REVERT: C 584 PHE cc_start: 0.7209 (m-80) cc_final: 0.6786 (m-80) REVERT: C 679 LYS cc_start: 0.9393 (ptmm) cc_final: 0.9048 (ptpp) REVERT: C 686 GLU cc_start: 0.8840 (tt0) cc_final: 0.8496 (pt0) REVERT: C 705 MET cc_start: 0.9207 (mtp) cc_final: 0.8654 (ptp) REVERT: C 737 MET cc_start: 0.6850 (ttp) cc_final: 0.6326 (ppp) REVERT: C 760 ASP cc_start: 0.7018 (t0) cc_final: 0.6694 (p0) REVERT: C 764 TYR cc_start: 0.6899 (m-10) cc_final: 0.6557 (m-80) REVERT: D 194 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7869 (pmt100) REVERT: D 248 MET cc_start: 0.8893 (mmm) cc_final: 0.8517 (mmm) REVERT: D 316 MET cc_start: 0.8735 (mmm) cc_final: 0.8237 (mmm) REVERT: D 584 PHE cc_start: 0.8516 (t80) cc_final: 0.8066 (t80) REVERT: D 606 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8113 (t80) REVERT: D 691 MET cc_start: 0.8801 (tmm) cc_final: 0.8186 (tmm) REVERT: D 722 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9045 (mp0) REVERT: D 780 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8525 (tp) REVERT: D 793 MET cc_start: 0.8835 (tpp) cc_final: 0.8547 (ttp) REVERT: D 861 MET cc_start: 0.6096 (mtt) cc_final: 0.5853 (mmm) outliers start: 73 outliers final: 37 residues processed: 300 average time/residue: 0.3771 time to fit residues: 186.8143 Evaluate side-chains 274 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 227 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 290 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS D 508 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28123 Z= 0.355 Angle : 0.929 13.426 38071 Z= 0.452 Chirality : 0.052 0.556 4412 Planarity : 0.006 0.124 4753 Dihedral : 16.176 109.809 4838 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.95 % Allowed : 15.95 % Favored : 83.10 % Rotamer: Outliers : 2.58 % Allowed : 13.84 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.62 % 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: -3.29 (0.14), residues: 3365 helix: -0.57 (0.13), residues: 1450 sheet: -4.32 (0.22), residues: 338 loop : -3.32 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 589 HIS 0.009 0.001 HIS D 253 PHE 0.037 0.002 PHE B 643 TYR 0.021 0.002 TYR C 454 ARG 0.007 0.001 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 240 time to evaluate : 3.117 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 85 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8958 (tm) REVERT: A 145 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.6947 (m-10) REVERT: A 298 MET cc_start: 0.8023 (tmm) cc_final: 0.7580 (tmm) REVERT: A 454 TYR cc_start: 0.8672 (m-80) cc_final: 0.8444 (m-80) REVERT: A 517 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8792 (mm) REVERT: A 565 MET cc_start: 0.8968 (ptt) cc_final: 0.8747 (ptt) REVERT: A 578 LEU cc_start: 0.9366 (pp) cc_final: 0.8825 (pp) REVERT: A 606 PHE cc_start: 0.8473 (m-80) cc_final: 0.8002 (t80) REVERT: A 612 PHE cc_start: 0.8826 (p90) cc_final: 0.8123 (p90) REVERT: A 620 MET cc_start: 0.8886 (mmm) cc_final: 0.8010 (mmm) REVERT: A 627 MET cc_start: 0.8706 (mmp) cc_final: 0.8310 (tpt) REVERT: A 691 MET cc_start: 0.8850 (ttp) cc_final: 0.8497 (ptm) REVERT: A 768 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7835 (p) REVERT: A 770 MET cc_start: 0.8631 (tpp) cc_final: 0.7427 (tpp) REVERT: A 824 PHE cc_start: 0.8656 (m-80) cc_final: 0.8390 (m-80) REVERT: B 55 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9130 (mm) REVERT: B 73 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.6586 (m110) REVERT: B 316 MET cc_start: 0.9309 (mmm) cc_final: 0.8935 (mmt) REVERT: B 651 TYR cc_start: 0.8991 (t80) cc_final: 0.8676 (t80) REVERT: B 719 LYS cc_start: 0.8955 (mttp) cc_final: 0.7906 (tppt) REVERT: B 770 MET cc_start: 0.6727 (tpt) cc_final: 0.6522 (tpp) REVERT: B 794 MET cc_start: 0.7268 (mmt) cc_final: 0.7010 (mmp) REVERT: C 339 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7347 (tp40) REVERT: C 413 MET cc_start: 0.7658 (ppp) cc_final: 0.6745 (ppp) REVERT: C 454 TYR cc_start: 0.8513 (m-80) cc_final: 0.8193 (m-80) REVERT: C 463 CYS cc_start: 0.9127 (m) cc_final: 0.8633 (m) REVERT: C 501 MET cc_start: 0.8827 (mpt) cc_final: 0.8244 (mmm) REVERT: C 556 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8372 (tt) REVERT: C 647 ILE cc_start: 0.8958 (mm) cc_final: 0.8680 (pt) REVERT: C 737 MET cc_start: 0.6576 (ttp) cc_final: 0.6095 (ppp) REVERT: C 743 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 760 ASP cc_start: 0.7077 (t0) cc_final: 0.6785 (p0) REVERT: C 764 TYR cc_start: 0.6848 (m-10) cc_final: 0.6501 (m-80) REVERT: D 248 MET cc_start: 0.8781 (mmm) cc_final: 0.8394 (mmm) REVERT: D 316 MET cc_start: 0.8877 (mmm) cc_final: 0.8557 (mmm) REVERT: D 584 PHE cc_start: 0.8566 (t80) cc_final: 0.8120 (t80) REVERT: D 606 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8231 (t80) REVERT: D 620 MET cc_start: 0.8483 (ttm) cc_final: 0.8243 (ttm) REVERT: D 691 MET cc_start: 0.8812 (tmm) cc_final: 0.8249 (tmm) REVERT: D 709 MET cc_start: 0.7708 (mmt) cc_final: 0.7501 (mpp) REVERT: D 780 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8615 (tp) REVERT: D 793 MET cc_start: 0.8795 (tpp) cc_final: 0.8435 (ttp) REVERT: D 861 MET cc_start: 0.6063 (mtt) cc_final: 0.5826 (mmm) outliers start: 72 outliers final: 46 residues processed: 296 average time/residue: 0.3583 time to fit residues: 175.8853 Evaluate side-chains 276 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 220 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 291 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28123 Z= 0.353 Angle : 0.917 13.724 38071 Z= 0.445 Chirality : 0.051 0.565 4412 Planarity : 0.005 0.129 4753 Dihedral : 15.105 108.779 4838 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.77 % Allowed : 16.43 % Favored : 82.80 % Rotamer: Outliers : 2.82 % Allowed : 14.45 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.59 % 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: -3.06 (0.14), residues: 3365 helix: -0.31 (0.13), residues: 1452 sheet: -4.27 (0.23), residues: 326 loop : -3.28 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 589 HIS 0.009 0.001 HIS D 253 PHE 0.038 0.002 PHE B 643 TYR 0.018 0.002 TYR C 454 ARG 0.005 0.001 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 226 time to evaluate : 3.461 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 85 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9143 (tm) REVERT: A 145 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: A 298 MET cc_start: 0.8066 (tmm) cc_final: 0.7629 (tmm) REVERT: A 316 MET cc_start: 0.8304 (mmm) cc_final: 0.7568 (tpt) REVERT: A 454 TYR cc_start: 0.8657 (m-80) cc_final: 0.8412 (m-80) REVERT: A 517 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8773 (mm) REVERT: A 534 MET cc_start: 0.8242 (pmm) cc_final: 0.7181 (pmm) REVERT: A 562 ASP cc_start: 0.7892 (m-30) cc_final: 0.7400 (t70) REVERT: A 578 LEU cc_start: 0.9368 (pp) cc_final: 0.8840 (pp) REVERT: A 606 PHE cc_start: 0.8526 (m-80) cc_final: 0.8082 (t80) REVERT: A 612 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8050 (p90) REVERT: A 620 MET cc_start: 0.8926 (mmm) cc_final: 0.8096 (mmm) REVERT: A 627 MET cc_start: 0.8639 (mmp) cc_final: 0.8110 (tpt) REVERT: A 691 MET cc_start: 0.8844 (ttp) cc_final: 0.8507 (ptm) REVERT: A 768 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7662 (p) REVERT: A 770 MET cc_start: 0.8609 (tpp) cc_final: 0.7362 (tpp) REVERT: A 794 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8204 (ttp) REVERT: A 824 PHE cc_start: 0.8596 (m-80) cc_final: 0.8344 (m-80) REVERT: B 55 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9081 (mm) REVERT: B 73 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6852 (m110) REVERT: B 651 TYR cc_start: 0.8986 (t80) cc_final: 0.8630 (t80) REVERT: B 680 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7168 (tp) REVERT: B 719 LYS cc_start: 0.8948 (mttp) cc_final: 0.7975 (tppt) REVERT: B 794 MET cc_start: 0.7290 (mmt) cc_final: 0.7034 (mmp) REVERT: C 250 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: C 413 MET cc_start: 0.7852 (ppp) cc_final: 0.6833 (ppp) REVERT: C 454 TYR cc_start: 0.8456 (m-80) cc_final: 0.8124 (m-80) REVERT: C 463 CYS cc_start: 0.9178 (m) cc_final: 0.8676 (m) REVERT: C 501 MET cc_start: 0.8901 (mpt) cc_final: 0.8252 (mmm) REVERT: C 556 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 647 ILE cc_start: 0.8957 (mm) cc_final: 0.8669 (pt) REVERT: C 686 GLU cc_start: 0.8368 (pt0) cc_final: 0.8158 (pt0) REVERT: C 737 MET cc_start: 0.6713 (ttp) cc_final: 0.6179 (ppp) REVERT: C 743 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8114 (mt-10) REVERT: C 760 ASP cc_start: 0.7179 (t0) cc_final: 0.6949 (p0) REVERT: C 764 TYR cc_start: 0.6726 (m-10) cc_final: 0.6392 (m-80) REVERT: C 794 MET cc_start: 0.8337 (ptm) cc_final: 0.8121 (ttm) REVERT: D 248 MET cc_start: 0.8799 (mmm) cc_final: 0.8473 (mmm) REVERT: D 316 MET cc_start: 0.8986 (mmm) cc_final: 0.8778 (mmm) REVERT: D 584 PHE cc_start: 0.8536 (t80) cc_final: 0.8107 (t80) REVERT: D 606 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8291 (t80) REVERT: D 691 MET cc_start: 0.8847 (tmm) cc_final: 0.8239 (tmm) REVERT: D 780 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8583 (tp) REVERT: D 793 MET cc_start: 0.8747 (tpp) cc_final: 0.8365 (ttp) REVERT: D 861 MET cc_start: 0.6029 (mtt) cc_final: 0.5790 (mmm) REVERT: D 867 MET cc_start: 0.7226 (ppp) cc_final: 0.6817 (ppp) outliers start: 79 outliers final: 51 residues processed: 283 average time/residue: 0.3601 time to fit residues: 168.2710 Evaluate side-chains 279 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 215 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 107 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28123 Z= 0.222 Angle : 0.862 14.256 38071 Z= 0.415 Chirality : 0.049 0.528 4412 Planarity : 0.005 0.128 4753 Dihedral : 14.125 103.728 4838 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.68 % Allowed : 14.85 % Favored : 84.46 % Rotamer: Outliers : 2.45 % Allowed : 14.65 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.52 % 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: -2.80 (0.14), residues: 3365 helix: -0.01 (0.13), residues: 1460 sheet: -4.13 (0.23), residues: 325 loop : -3.24 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 589 HIS 0.007 0.001 HIS D 253 PHE 0.039 0.002 PHE B 643 TYR 0.018 0.001 TYR C 454 ARG 0.006 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 239 time to evaluate : 3.239 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 85 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8983 (tm) REVERT: A 145 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.6935 (m-10) REVERT: A 298 MET cc_start: 0.8022 (tmm) cc_final: 0.7545 (tmm) REVERT: A 316 MET cc_start: 0.8353 (mmm) cc_final: 0.7596 (tpt) REVERT: A 360 MET cc_start: 0.9133 (mmm) cc_final: 0.8875 (mmm) REVERT: A 454 TYR cc_start: 0.8663 (m-80) cc_final: 0.8379 (m-80) REVERT: A 517 LEU cc_start: 0.9125 (mm) cc_final: 0.8744 (mm) REVERT: A 534 MET cc_start: 0.8153 (pmm) cc_final: 0.7135 (pmm) REVERT: A 562 ASP cc_start: 0.8030 (m-30) cc_final: 0.7528 (t70) REVERT: A 578 LEU cc_start: 0.9367 (pp) cc_final: 0.8811 (pp) REVERT: A 606 PHE cc_start: 0.8443 (m-80) cc_final: 0.7993 (t80) REVERT: A 612 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8030 (p90) REVERT: A 627 MET cc_start: 0.8584 (mmp) cc_final: 0.8041 (tpt) REVERT: A 691 MET cc_start: 0.8823 (ttp) cc_final: 0.8456 (ptm) REVERT: A 768 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7464 (p) REVERT: A 770 MET cc_start: 0.8744 (tpp) cc_final: 0.7312 (tpp) REVERT: B 50 MET cc_start: 0.7601 (tmm) cc_final: 0.7238 (tmm) REVERT: B 55 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 651 TYR cc_start: 0.8899 (t80) cc_final: 0.8442 (t80) REVERT: B 680 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7089 (tp) REVERT: B 682 TYR cc_start: 0.5527 (OUTLIER) cc_final: 0.5176 (m-80) REVERT: B 719 LYS cc_start: 0.8970 (mttp) cc_final: 0.7920 (tppt) REVERT: B 794 MET cc_start: 0.7320 (mmt) cc_final: 0.7068 (mmp) REVERT: C 250 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: C 413 MET cc_start: 0.7719 (ppp) cc_final: 0.6756 (ppp) REVERT: C 441 GLU cc_start: 0.8485 (tp30) cc_final: 0.8146 (mp0) REVERT: C 454 TYR cc_start: 0.8363 (m-80) cc_final: 0.8048 (m-80) REVERT: C 463 CYS cc_start: 0.9152 (m) cc_final: 0.8741 (m) REVERT: C 501 MET cc_start: 0.8864 (mpt) cc_final: 0.8175 (mmm) REVERT: C 627 MET cc_start: 0.7182 (mmp) cc_final: 0.6923 (mmp) REVERT: C 647 ILE cc_start: 0.8962 (mm) cc_final: 0.8673 (pt) REVERT: C 737 MET cc_start: 0.6696 (ttp) cc_final: 0.6236 (ppp) REVERT: C 743 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 764 TYR cc_start: 0.6536 (m-10) cc_final: 0.6184 (m-80) REVERT: D 248 MET cc_start: 0.8798 (mmm) cc_final: 0.8557 (mmm) REVERT: D 584 PHE cc_start: 0.8453 (t80) cc_final: 0.7753 (t80) REVERT: D 691 MET cc_start: 0.8791 (tmm) cc_final: 0.8178 (tmm) REVERT: D 709 MET cc_start: 0.7906 (mmt) cc_final: 0.7596 (mpp) REVERT: D 770 MET cc_start: 0.7866 (mmm) cc_final: 0.7658 (mmp) REVERT: D 780 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8524 (tp) REVERT: D 793 MET cc_start: 0.8658 (tpp) cc_final: 0.8382 (ttp) REVERT: D 861 MET cc_start: 0.6025 (mtt) cc_final: 0.5707 (mmm) REVERT: D 867 MET cc_start: 0.7173 (ppp) cc_final: 0.6765 (ppp) outliers start: 68 outliers final: 39 residues processed: 289 average time/residue: 0.3685 time to fit residues: 177.7374 Evaluate side-chains 261 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 149 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28123 Z= 0.230 Angle : 0.862 14.774 38071 Z= 0.413 Chirality : 0.050 0.518 4412 Planarity : 0.005 0.130 4753 Dihedral : 13.521 101.662 4838 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.91 % Favored : 84.46 % Rotamer: Outliers : 2.21 % Allowed : 15.30 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.52 % 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: -2.66 (0.14), residues: 3365 helix: 0.10 (0.14), residues: 1466 sheet: -4.02 (0.24), residues: 325 loop : -3.19 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 589 HIS 0.006 0.001 HIS D 253 PHE 0.064 0.002 PHE B 643 TYR 0.019 0.001 TYR C 252 ARG 0.006 0.000 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 3.157 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 85 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8996 (tm) REVERT: A 145 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: A 298 MET cc_start: 0.8045 (tmm) cc_final: 0.7554 (tmm) REVERT: A 316 MET cc_start: 0.8340 (mmm) cc_final: 0.7587 (tpt) REVERT: A 454 TYR cc_start: 0.8677 (m-80) cc_final: 0.8357 (m-80) REVERT: A 517 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 534 MET cc_start: 0.8180 (pmm) cc_final: 0.7162 (pmm) REVERT: A 562 ASP cc_start: 0.7993 (m-30) cc_final: 0.7534 (t70) REVERT: A 578 LEU cc_start: 0.9376 (pp) cc_final: 0.8853 (pp) REVERT: A 606 PHE cc_start: 0.8471 (m-80) cc_final: 0.8032 (t80) REVERT: A 612 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7994 (p90) REVERT: A 620 MET cc_start: 0.8894 (mmm) cc_final: 0.8390 (mmm) REVERT: A 627 MET cc_start: 0.8569 (mmp) cc_final: 0.7935 (tpp) REVERT: A 691 MET cc_start: 0.8792 (ttp) cc_final: 0.8415 (ptm) REVERT: A 714 GLN cc_start: 0.7417 (tp-100) cc_final: 0.7212 (tp-100) REVERT: A 768 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7517 (p) REVERT: A 770 MET cc_start: 0.8783 (tpp) cc_final: 0.7582 (tpp) REVERT: B 55 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8977 (mm) REVERT: B 589 TRP cc_start: 0.6411 (OUTLIER) cc_final: 0.6057 (m100) REVERT: B 639 ILE cc_start: 0.8895 (mm) cc_final: 0.8666 (mt) REVERT: B 651 TYR cc_start: 0.8906 (t80) cc_final: 0.8473 (t80) REVERT: B 680 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7095 (tp) REVERT: B 719 LYS cc_start: 0.8973 (mttp) cc_final: 0.7922 (tppt) REVERT: B 794 MET cc_start: 0.7289 (mmt) cc_final: 0.7045 (mmp) REVERT: C 196 ASN cc_start: 0.7231 (m110) cc_final: 0.7012 (m-40) REVERT: C 360 MET cc_start: 0.9107 (mmm) cc_final: 0.8878 (mmm) REVERT: C 413 MET cc_start: 0.7743 (ppp) cc_final: 0.6780 (ppp) REVERT: C 454 TYR cc_start: 0.8374 (m-80) cc_final: 0.8087 (m-80) REVERT: C 463 CYS cc_start: 0.9177 (m) cc_final: 0.8714 (m) REVERT: C 501 MET cc_start: 0.8885 (mpt) cc_final: 0.8213 (mmm) REVERT: C 559 LEU cc_start: 0.9163 (mt) cc_final: 0.8900 (tp) REVERT: C 737 MET cc_start: 0.6655 (ttp) cc_final: 0.6199 (ppp) REVERT: C 743 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8126 (mt-10) REVERT: C 764 TYR cc_start: 0.6489 (m-10) cc_final: 0.6145 (m-80) REVERT: D 248 MET cc_start: 0.8792 (mmm) cc_final: 0.8562 (mmm) REVERT: D 691 MET cc_start: 0.8813 (tmm) cc_final: 0.8161 (tmm) REVERT: D 770 MET cc_start: 0.7910 (mmm) cc_final: 0.7686 (mmp) REVERT: D 861 MET cc_start: 0.5931 (mtt) cc_final: 0.5716 (mmm) REVERT: D 867 MET cc_start: 0.7253 (ppp) cc_final: 0.6856 (ppp) outliers start: 61 outliers final: 40 residues processed: 277 average time/residue: 0.3590 time to fit residues: 167.0250 Evaluate side-chains 264 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.5980 chunk 129 optimal weight: 20.0000 chunk 193 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 254 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 ASN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28123 Z= 0.204 Angle : 0.855 14.176 38071 Z= 0.409 Chirality : 0.049 0.493 4412 Planarity : 0.005 0.118 4753 Dihedral : 12.761 100.970 4838 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.57 % Allowed : 14.02 % Favored : 85.42 % Rotamer: Outliers : 1.94 % Allowed : 15.74 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.49 % 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: -2.50 (0.14), residues: 3365 helix: 0.23 (0.14), residues: 1461 sheet: -3.88 (0.24), residues: 321 loop : -3.11 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 706 HIS 0.007 0.001 HIS A 792 PHE 0.055 0.002 PHE B 643 TYR 0.016 0.001 TYR C 252 ARG 0.006 0.000 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 249 time to evaluate : 3.013 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 85 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8941 (tm) REVERT: A 145 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.6849 (m-10) REVERT: A 171 THR cc_start: 0.8344 (m) cc_final: 0.8065 (t) REVERT: A 298 MET cc_start: 0.8057 (tmm) cc_final: 0.7549 (tmm) REVERT: A 316 MET cc_start: 0.8325 (mmm) cc_final: 0.7596 (tpt) REVERT: A 360 MET cc_start: 0.9088 (mmm) cc_final: 0.8592 (mmm) REVERT: A 454 TYR cc_start: 0.8681 (m-80) cc_final: 0.8367 (m-80) REVERT: A 501 MET cc_start: 0.8463 (mmt) cc_final: 0.8250 (mmp) REVERT: A 517 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8752 (mm) REVERT: A 534 MET cc_start: 0.8234 (pmm) cc_final: 0.7254 (pmm) REVERT: A 562 ASP cc_start: 0.7982 (m-30) cc_final: 0.7534 (t70) REVERT: A 612 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8017 (p90) REVERT: A 620 MET cc_start: 0.8910 (mmm) cc_final: 0.8618 (mmm) REVERT: A 627 MET cc_start: 0.8536 (mmp) cc_final: 0.7885 (tpp) REVERT: A 691 MET cc_start: 0.8771 (ttp) cc_final: 0.8358 (ptm) REVERT: A 770 MET cc_start: 0.8788 (tpp) cc_final: 0.7558 (tpp) REVERT: A 867 MET cc_start: 0.6313 (ttp) cc_final: 0.5722 (tpt) REVERT: B 254 TYR cc_start: 0.8589 (m-80) cc_final: 0.8275 (m-80) REVERT: B 589 TRP cc_start: 0.6290 (OUTLIER) cc_final: 0.5948 (m100) REVERT: B 639 ILE cc_start: 0.8915 (mm) cc_final: 0.8713 (mt) REVERT: B 651 TYR cc_start: 0.8875 (t80) cc_final: 0.8572 (t80) REVERT: B 680 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7253 (tp) REVERT: B 719 LYS cc_start: 0.8966 (mttp) cc_final: 0.7906 (tppt) REVERT: B 794 MET cc_start: 0.7328 (mmt) cc_final: 0.7078 (mmp) REVERT: C 196 ASN cc_start: 0.6956 (m110) cc_final: 0.6754 (m-40) REVERT: C 413 MET cc_start: 0.7689 (ppp) cc_final: 0.6765 (ppp) REVERT: C 454 TYR cc_start: 0.8456 (m-80) cc_final: 0.8159 (m-80) REVERT: C 463 CYS cc_start: 0.9107 (m) cc_final: 0.8568 (m) REVERT: C 484 GLU cc_start: 0.8464 (mp0) cc_final: 0.7864 (tp30) REVERT: C 501 MET cc_start: 0.8923 (mpt) cc_final: 0.8210 (mmm) REVERT: C 647 ILE cc_start: 0.8934 (mm) cc_final: 0.8645 (pt) REVERT: C 737 MET cc_start: 0.6667 (ttp) cc_final: 0.6222 (ppp) REVERT: C 743 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8337 (mt-10) REVERT: C 764 TYR cc_start: 0.6349 (m-10) cc_final: 0.6038 (m-80) REVERT: C 815 LEU cc_start: 0.8449 (mt) cc_final: 0.8002 (mt) REVERT: D 248 MET cc_start: 0.8746 (mmm) cc_final: 0.8482 (mmm) REVERT: D 620 MET cc_start: 0.8384 (ttm) cc_final: 0.7820 (ttm) REVERT: D 621 GLN cc_start: 0.8773 (mp10) cc_final: 0.8516 (mp10) REVERT: D 691 MET cc_start: 0.8811 (tmm) cc_final: 0.8133 (tmm) REVERT: D 793 MET cc_start: 0.8675 (tpp) cc_final: 0.8313 (ttp) REVERT: D 861 MET cc_start: 0.6098 (mtt) cc_final: 0.5677 (mmm) outliers start: 53 outliers final: 37 residues processed: 289 average time/residue: 0.3552 time to fit residues: 171.4241 Evaluate side-chains 272 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 30.0000 chunk 310 optimal weight: 4.9990 chunk 283 optimal weight: 0.0270 chunk 301 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 0.0170 chunk 236 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28123 Z= 0.222 Angle : 0.860 16.039 38071 Z= 0.410 Chirality : 0.049 0.487 4412 Planarity : 0.005 0.118 4753 Dihedral : 12.224 104.320 4838 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.57 % Allowed : 14.20 % Favored : 85.24 % Rotamer: Outliers : 1.77 % Allowed : 16.22 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.49 % 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: -2.42 (0.15), residues: 3365 helix: 0.30 (0.14), residues: 1473 sheet: -3.87 (0.24), residues: 323 loop : -3.07 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 134 HIS 0.007 0.001 HIS A 792 PHE 0.050 0.002 PHE B 643 TYR 0.019 0.001 TYR D 702 ARG 0.013 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 236 time to evaluate : 3.295 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: A 85 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8873 (tm) REVERT: A 145 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.6859 (m-10) REVERT: A 171 THR cc_start: 0.8353 (m) cc_final: 0.8084 (t) REVERT: A 298 MET cc_start: 0.8090 (tmm) cc_final: 0.7573 (tmm) REVERT: A 316 MET cc_start: 0.8434 (mmm) cc_final: 0.7620 (tpt) REVERT: A 454 TYR cc_start: 0.8550 (m-80) cc_final: 0.8279 (m-80) REVERT: A 517 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8744 (mm) REVERT: A 534 MET cc_start: 0.8261 (pmm) cc_final: 0.7284 (pmm) REVERT: A 562 ASP cc_start: 0.7919 (m-30) cc_final: 0.7471 (t70) REVERT: A 606 PHE cc_start: 0.8542 (m-80) cc_final: 0.8047 (t80) REVERT: A 612 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8004 (p90) REVERT: A 627 MET cc_start: 0.8518 (mmp) cc_final: 0.7859 (tpp) REVERT: A 691 MET cc_start: 0.8795 (ttp) cc_final: 0.8350 (ptm) REVERT: A 770 MET cc_start: 0.8765 (tpp) cc_final: 0.7541 (tpp) REVERT: B 491 GLN cc_start: 0.6111 (tm-30) cc_final: 0.5854 (mt0) REVERT: B 589 TRP cc_start: 0.6266 (OUTLIER) cc_final: 0.5932 (m100) REVERT: B 651 TYR cc_start: 0.8878 (t80) cc_final: 0.8590 (t80) REVERT: B 680 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7296 (tp) REVERT: B 719 LYS cc_start: 0.8964 (mttp) cc_final: 0.7906 (tppt) REVERT: B 794 MET cc_start: 0.7310 (mmt) cc_final: 0.7064 (mmp) REVERT: C 413 MET cc_start: 0.7720 (ppp) cc_final: 0.6777 (ppp) REVERT: C 454 TYR cc_start: 0.8452 (m-80) cc_final: 0.8164 (m-80) REVERT: C 463 CYS cc_start: 0.9135 (m) cc_final: 0.8611 (m) REVERT: C 484 GLU cc_start: 0.8326 (mp0) cc_final: 0.7810 (tp30) REVERT: C 501 MET cc_start: 0.8943 (mpt) cc_final: 0.8388 (mmt) REVERT: C 556 LEU cc_start: 0.8711 (mm) cc_final: 0.8321 (mt) REVERT: C 559 LEU cc_start: 0.9136 (mt) cc_final: 0.8898 (tp) REVERT: C 679 LYS cc_start: 0.9346 (ptmm) cc_final: 0.8879 (ptpp) REVERT: C 737 MET cc_start: 0.6645 (ttp) cc_final: 0.6234 (ppp) REVERT: C 764 TYR cc_start: 0.6447 (m-10) cc_final: 0.6207 (m-80) REVERT: C 770 MET cc_start: 0.9051 (tpp) cc_final: 0.8824 (tpp) REVERT: C 815 LEU cc_start: 0.8476 (mt) cc_final: 0.8028 (mt) REVERT: D 248 MET cc_start: 0.8698 (mmm) cc_final: 0.8356 (mmm) REVERT: D 620 MET cc_start: 0.8408 (ttm) cc_final: 0.8038 (ttm) REVERT: D 691 MET cc_start: 0.8797 (tmm) cc_final: 0.8120 (tmm) REVERT: D 793 MET cc_start: 0.8591 (tpp) cc_final: 0.8232 (ptt) REVERT: D 861 MET cc_start: 0.6101 (mtt) cc_final: 0.5684 (mmm) outliers start: 48 outliers final: 40 residues processed: 270 average time/residue: 0.4096 time to fit residues: 187.5620 Evaluate side-chains 272 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 3.9990 chunk 319 optimal weight: 0.0770 chunk 194 optimal weight: 1.9990 chunk 151 optimal weight: 0.0170 chunk 221 optimal weight: 8.9990 chunk 334 optimal weight: 8.9990 chunk 308 optimal weight: 0.9990 chunk 266 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 205 optimal weight: 0.0980 chunk 163 optimal weight: 2.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN C 232 HIS C 286 ASN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28123 Z= 0.189 Angle : 0.866 16.909 38071 Z= 0.410 Chirality : 0.049 0.463 4412 Planarity : 0.005 0.113 4753 Dihedral : 11.545 107.887 4838 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.80 % Favored : 86.67 % Rotamer: Outliers : 1.56 % Allowed : 16.35 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.40 % 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: -2.33 (0.15), residues: 3365 helix: 0.32 (0.14), residues: 1473 sheet: -3.67 (0.25), residues: 320 loop : -3.01 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 134 HIS 0.008 0.001 HIS A 792 PHE 0.049 0.002 PHE B 643 TYR 0.017 0.001 TYR D 462 ARG 0.006 0.000 ARG B 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 251 time to evaluate : 3.092 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 85 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8723 (tm) REVERT: A 145 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: A 171 THR cc_start: 0.8198 (m) cc_final: 0.7912 (t) REVERT: A 298 MET cc_start: 0.8092 (tmm) cc_final: 0.7618 (tmm) REVERT: A 316 MET cc_start: 0.8303 (mmm) cc_final: 0.7552 (tpt) REVERT: A 360 MET cc_start: 0.9052 (mmm) cc_final: 0.8596 (mmm) REVERT: A 454 TYR cc_start: 0.8614 (m-80) cc_final: 0.8322 (m-80) REVERT: A 501 MET cc_start: 0.8496 (mmp) cc_final: 0.8242 (mmt) REVERT: A 517 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8700 (mm) REVERT: A 534 MET cc_start: 0.8210 (pmm) cc_final: 0.7194 (pmm) REVERT: A 562 ASP cc_start: 0.7926 (m-30) cc_final: 0.7458 (t70) REVERT: A 612 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7919 (p90) REVERT: A 620 MET cc_start: 0.8816 (mmm) cc_final: 0.8347 (tpp) REVERT: A 627 MET cc_start: 0.8519 (mmp) cc_final: 0.7879 (tpp) REVERT: A 691 MET cc_start: 0.8871 (ttp) cc_final: 0.8361 (ptm) REVERT: A 770 MET cc_start: 0.8744 (tpp) cc_final: 0.7834 (tpp) REVERT: A 867 MET cc_start: 0.6787 (ptt) cc_final: 0.5689 (tpt) REVERT: B 254 TYR cc_start: 0.8351 (m-80) cc_final: 0.8082 (m-80) REVERT: B 491 GLN cc_start: 0.5771 (tm-30) cc_final: 0.5398 (mt0) REVERT: B 589 TRP cc_start: 0.6144 (OUTLIER) cc_final: 0.5836 (m100) REVERT: B 651 TYR cc_start: 0.8797 (t80) cc_final: 0.8262 (t80) REVERT: B 680 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7265 (tp) REVERT: B 719 LYS cc_start: 0.8932 (mttp) cc_final: 0.7843 (tppt) REVERT: B 794 MET cc_start: 0.7275 (mmt) cc_final: 0.7041 (mmp) REVERT: B 867 MET cc_start: 0.6706 (tmm) cc_final: 0.5850 (mmt) REVERT: C 171 THR cc_start: 0.8199 (p) cc_final: 0.7916 (p) REVERT: C 323 MET cc_start: 0.9393 (mmm) cc_final: 0.9188 (tpp) REVERT: C 360 MET cc_start: 0.9010 (mmm) cc_final: 0.8809 (mmm) REVERT: C 413 MET cc_start: 0.7608 (ppp) cc_final: 0.6725 (ppp) REVERT: C 426 ASP cc_start: 0.8876 (m-30) cc_final: 0.8643 (t0) REVERT: C 454 TYR cc_start: 0.8422 (m-80) cc_final: 0.8132 (m-80) REVERT: C 463 CYS cc_start: 0.9120 (m) cc_final: 0.8624 (m) REVERT: C 484 GLU cc_start: 0.8294 (mp0) cc_final: 0.7812 (tp30) REVERT: C 501 MET cc_start: 0.8934 (mpt) cc_final: 0.8250 (mmm) REVERT: C 556 LEU cc_start: 0.8575 (mm) cc_final: 0.8225 (mp) REVERT: C 559 LEU cc_start: 0.9141 (mt) cc_final: 0.8879 (tp) REVERT: C 647 ILE cc_start: 0.8917 (mm) cc_final: 0.8626 (pt) REVERT: C 737 MET cc_start: 0.6697 (ttp) cc_final: 0.6379 (ppp) REVERT: C 764 TYR cc_start: 0.6251 (m-10) cc_final: 0.5985 (m-80) REVERT: C 770 MET cc_start: 0.8934 (tpp) cc_final: 0.8634 (tpp) REVERT: C 815 LEU cc_start: 0.8424 (mt) cc_final: 0.7975 (mt) REVERT: D 248 MET cc_start: 0.8617 (mmm) cc_final: 0.8362 (mmm) REVERT: D 620 MET cc_start: 0.8379 (ttm) cc_final: 0.7939 (ttm) REVERT: D 621 GLN cc_start: 0.8807 (mp10) cc_final: 0.8528 (mp10) REVERT: D 691 MET cc_start: 0.8753 (tmm) cc_final: 0.8042 (tmm) REVERT: D 726 GLN cc_start: 0.9356 (mt0) cc_final: 0.8931 (tm-30) REVERT: D 793 MET cc_start: 0.8624 (tpp) cc_final: 0.8254 (ptt) REVERT: D 861 MET cc_start: 0.6122 (mtt) cc_final: 0.5713 (mmm) REVERT: D 867 MET cc_start: 0.7382 (ppp) cc_final: 0.6924 (ppp) outliers start: 42 outliers final: 31 residues processed: 283 average time/residue: 0.3720 time to fit residues: 175.3440 Evaluate side-chains 272 residues out of total 2931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 796 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 245 optimal weight: 0.0470 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 49 optimal weight: 7.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 196 ASN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.104206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072325 restraints weight = 169463.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073490 restraints weight = 81224.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.073851 restraints weight = 58386.581| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28123 Z= 0.190 Angle : 0.856 14.410 38071 Z= 0.404 Chirality : 0.048 0.444 4412 Planarity : 0.005 0.110 4753 Dihedral : 11.072 108.192 4838 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.21 % Favored : 86.31 % Rotamer: Outliers : 1.56 % Allowed : 16.66 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.37 % 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: -2.21 (0.15), residues: 3365 helix: 0.41 (0.14), residues: 1473 sheet: -3.57 (0.26), residues: 311 loop : -2.96 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 134 HIS 0.012 0.001 HIS C 111 PHE 0.050 0.002 PHE B 643 TYR 0.018 0.001 TYR D 702 ARG 0.005 0.000 ARG D 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5158.60 seconds wall clock time: 96 minutes 48.28 seconds (5808.28 seconds total)