Starting phenix.real_space_refine on Mon Mar 18 04:25:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/03_2024/8sau_40280_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/03_2024/8sau_40280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/03_2024/8sau_40280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/03_2024/8sau_40280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/03_2024/8sau_40280_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/03_2024/8sau_40280_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 138 5.16 5 C 12429 2.51 5 N 3321 2.21 5 O 3996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "G ASP 632": "OD1" <-> "OD2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "L ASP 632": "OD1" <-> "OD2" Residue "L GLU 634": "OE1" <-> "OE2" Residue "L ASP 659": "OD1" <-> "OD2" Residue "M ASP 63": "OD1" <-> "OD2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 28": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19884 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "S" 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: "T" 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.69, per 1000 atoms: 0.54 Number of scatterers: 19884 At special positions: 0 Unit cell: (157.768, 158.834, 137.514, 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 138 16.00 O 3996 8.00 N 3321 7.00 C 12429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.06 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.05 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.04 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " distance=2.04 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 7.73 Conformation dependent library (CDL) restraints added in 3.1 seconds 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 41 sheets defined 20.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.535A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.575A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.670A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.696A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 571 through 596 removed outlier: 4.015A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.055A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.365A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 57 through 61 removed outlier: 3.630A pdb=" N ALA F 60 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 99 through 116 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 350 removed outlier: 3.607A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.665A pdb=" N THR F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 481 removed outlier: 3.654A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 543 through 545 No H-bonds generated for 'chain 'G' and resid 543 through 545' Processing helix chain 'G' and resid 572 through 596 removed outlier: 3.674A pdb=" N LEU G 576 " --> pdb=" O GLY G 572 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.128A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 4.346A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 645 " --> pdb=" O ILE G 641 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU G 661 " --> pdb=" O GLU G 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 57 through 61 removed outlier: 3.568A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 3.511A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 116 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 350 removed outlier: 3.556A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.609A pdb=" N THR K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 481 removed outlier: 3.614A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 484 No H-bonds generated for 'chain 'K' and resid 482 through 484' Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 543 through 545 No H-bonds generated for 'chain 'L' and resid 543 through 545' Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.864A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.013A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 4.477A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU L 645 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN L 650 " --> pdb=" O LEU L 646 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU L 661 " --> pdb=" O GLU L 657 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.729A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.017A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.738A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.653A pdb=" N GLU A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 260 current: chain 'A' and resid 284 through 302 removed outlier: 7.716A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 382 through 385 removed outlier: 4.518A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 413 through 421 current: chain 'A' and resid 468 through 470 Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.510A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 82 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 69 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 39 removed outlier: 6.634A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 60 current: chain 'C' and resid 116 through 117 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.906A pdb=" N GLY D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.948A pdb=" N TYR D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN D 39 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 38 " --> pdb=" O TYR D 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 494 through 499 removed outlier: 3.551A pdb=" N THR F 499 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP F 35 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.624A pdb=" N LYS F 46 " --> pdb=" O LYS F 490 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.692A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 173 through 176 Processing sheet with id=AC2, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 308 removed outlier: 6.623A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 316 through 323 current: chain 'F' and resid 382 through 385 removed outlier: 4.539A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 413 through 421 current: chain 'F' and resid 468 through 470 Processing sheet with id=AC4, first strand: chain 'F' and resid 423 through 425 Processing sheet with id=AC5, first strand: chain 'H' and resid 2 through 3 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 22 removed outlier: 4.023A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 32 through 39 removed outlier: 6.618A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 116 through 117 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.661A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 19 through 23 Processing sheet with id=AD1, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.026A pdb=" N TYR I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN I 39 " --> pdb=" O TYR I 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 494 through 499 removed outlier: 3.875A pdb=" N THR K 499 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP K 35 " --> pdb=" O THR K 499 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.641A pdb=" N LYS K 46 " --> pdb=" O LYS K 490 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.834A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 169 through 176 removed outlier: 4.562A pdb=" N ASN K 156 " --> pdb=" O SER K 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 260 current: chain 'K' and resid 284 through 302 removed outlier: 7.712A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL K 295 " --> pdb=" O ASN K 332 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 330 through 334 current: chain 'K' and resid 382 through 385 removed outlier: 4.482A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 413 through 421 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD8, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AD9, first strand: chain 'K' and resid 423 through 425 Processing sheet with id=AE1, first strand: chain 'M' and resid 18 through 22 removed outlier: 3.946A pdb=" N GLU M 82 " --> pdb=" O THR M 69 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR M 69 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 32 through 39 removed outlier: 6.661A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 58 through 60 current: chain 'M' and resid 116 through 117 Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.773A pdb=" N GLY N 12 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'N' and resid 48 through 50 removed outlier: 3.633A pdb=" N ILE N 50 " --> pdb=" O TRP N 37 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE N 38 " --> pdb=" O TYR N 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR N 89 " --> pdb=" O PHE N 38 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1356 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: 6.67 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6339 1.35 - 1.48: 5389 1.48 - 1.61: 8402 1.61 - 1.74: 3 1.74 - 1.86: 183 Bond restraints: 20316 Sorted by residual: bond pdb=" CA GLN I 39 " pdb=" CB GLN I 39 " ideal model delta sigma weight residual 1.526 1.600 -0.074 1.70e-02 3.46e+03 1.91e+01 bond pdb=" CB CYS K 433 " pdb=" SG CYS K 433 " ideal model delta sigma weight residual 1.808 1.706 0.102 3.30e-02 9.18e+02 9.64e+00 bond pdb=" CB CYS F 433 " pdb=" SG CYS F 433 " ideal model delta sigma weight residual 1.808 1.715 0.093 3.30e-02 9.18e+02 7.96e+00 bond pdb=" C5 MAN V 7 " pdb=" O5 MAN V 7 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C5 MAN R 7 " pdb=" O5 MAN R 7 " ideal model delta sigma weight residual 1.418 1.470 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 20311 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.76: 412 105.76 - 112.85: 10969 112.85 - 119.93: 6928 119.93 - 127.02: 8996 127.02 - 134.10: 331 Bond angle restraints: 27636 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 133.92 -12.22 1.80e+00 3.09e-01 4.61e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 133.53 -11.83 1.80e+00 3.09e-01 4.32e+01 angle pdb=" C SER M 25 " pdb=" N GLY M 26 " pdb=" CA GLY M 26 " ideal model delta sigma weight residual 121.70 131.44 -9.74 1.80e+00 3.09e-01 2.93e+01 angle pdb=" C SER C 25 " pdb=" N GLY C 26 " pdb=" CA GLY C 26 " ideal model delta sigma weight residual 121.70 131.35 -9.65 1.80e+00 3.09e-01 2.88e+01 ... (remaining 27631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 11866 22.14 - 44.27: 782 44.27 - 66.41: 87 66.41 - 88.55: 80 88.55 - 110.68: 43 Dihedral angle restraints: 12858 sinusoidal: 5763 harmonic: 7095 Sorted by residual: dihedral pdb=" CA VAL G 570 " pdb=" C VAL G 570 " pdb=" N TRP G 571 " pdb=" CA TRP G 571 " ideal model delta harmonic sigma weight residual 180.00 143.21 36.79 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" CA GLY K 431 " pdb=" C GLY K 431 " pdb=" N ARG K 432 " pdb=" CA ARG K 432 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA GLY F 431 " pdb=" C GLY F 431 " pdb=" N ARG F 432 " pdb=" CA ARG F 432 " ideal model delta harmonic sigma weight residual 180.00 -146.65 -33.35 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 12855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2715 0.067 - 0.133: 474 0.133 - 0.200: 60 0.200 - 0.267: 5 0.267 - 0.333: 7 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.04e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.74e+00 ... (remaining 3258 not shown) Planarity restraints: 3465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 252 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 253 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 252 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO K 253 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.022 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP F 112 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.000 2.00e-02 2.50e+03 ... (remaining 3462 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 243 2.63 - 3.20: 18003 3.20 - 3.77: 28629 3.77 - 4.33: 41696 4.33 - 4.90: 67547 Nonbonded interactions: 156118 Sorted by model distance: nonbonded pdb=" O LEU K 84 " pdb=" OG SER K 243 " model vdw 2.063 2.440 nonbonded pdb=" OE2 GLU K 83 " pdb=" OG SER K 243 " model vdw 2.065 2.440 nonbonded pdb=" O LYS A 360 " pdb=" OG1 THR A 467 " model vdw 2.068 2.440 nonbonded pdb=" O LYS F 360 " pdb=" OG1 THR F 467 " model vdw 2.070 2.440 nonbonded pdb=" OE2 GLU A 83 " pdb=" OG SER A 243 " model vdw 2.088 2.440 ... (remaining 156113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.560 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 52.550 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.006 0.102 20316 Z= 0.404 Angle : 0.993 12.219 27636 Z= 0.518 Chirality : 0.054 0.333 3261 Planarity : 0.006 0.111 3453 Dihedral : 16.966 110.682 8181 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.17 % Favored : 92.51 % Rotamer: Outliers : 0.05 % Allowed : 0.09 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.22 (0.16), residues: 2442 helix: -1.57 (0.23), residues: 444 sheet: -1.18 (0.19), residues: 642 loop : -1.56 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP F 112 HIS 0.012 0.002 HIS A 105 PHE 0.031 0.002 PHE M 114 TYR 0.029 0.003 TYR D 48 ARG 0.016 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 560 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.7683 (t0) cc_final: 0.7284 (m-30) REVERT: B 617 ARG cc_start: 0.7543 (mtp180) cc_final: 0.6909 (ttm-80) REVERT: B 629 LEU cc_start: 0.7521 (tp) cc_final: 0.6896 (pp) REVERT: F 104 MET cc_start: 0.8541 (ttt) cc_final: 0.8298 (ttt) REVERT: F 114 GLN cc_start: 0.7660 (tt0) cc_final: 0.7304 (mp10) REVERT: F 344 LYS cc_start: 0.7914 (mttt) cc_final: 0.7617 (mttm) REVERT: F 426 MET cc_start: 0.5396 (mtm) cc_final: 0.5120 (mtp) REVERT: G 625 ASN cc_start: 0.7444 (p0) cc_final: 0.7184 (t0) REVERT: G 629 LEU cc_start: 0.7456 (tp) cc_final: 0.7242 (tp) REVERT: G 659 ASP cc_start: 0.7992 (m-30) cc_final: 0.7583 (m-30) REVERT: I 35 VAL cc_start: 0.8092 (t) cc_final: 0.7861 (p) REVERT: K 113 ASP cc_start: 0.8019 (t0) cc_final: 0.7755 (m-30) REVERT: K 114 GLN cc_start: 0.7500 (tt0) cc_final: 0.7058 (tt0) REVERT: K 340 ASP cc_start: 0.7988 (t0) cc_final: 0.7668 (m-30) REVERT: K 371 ILE cc_start: 0.7369 (mt) cc_final: 0.6879 (mt) REVERT: N 80 LEU cc_start: 0.6086 (mp) cc_final: 0.5854 (tt) outliers start: 1 outliers final: 0 residues processed: 561 average time/residue: 0.3094 time to fit residues: 261.9395 Evaluate side-chains 350 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 287 HIS C 52 ASN C 60 ASN ** D 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS F 241 ASN F 287 HIS G 590 GLN H 113 ASN H 116 HIS I 62 HIS K 241 ASN K 287 HIS L 543 ASN L 640 GLN L 653 GLN M 119 GLN N 62 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 20316 Z= 0.353 Angle : 0.792 16.137 27636 Z= 0.405 Chirality : 0.052 0.309 3261 Planarity : 0.005 0.079 3453 Dihedral : 12.883 97.638 3777 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.98 % Favored : 93.69 % Rotamer: Outliers : 2.72 % Allowed : 10.75 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2442 helix: -0.79 (0.25), residues: 429 sheet: -1.23 (0.18), residues: 690 loop : -1.62 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 112 HIS 0.008 0.002 HIS N 62 PHE 0.024 0.002 PHE C 64 TYR 0.022 0.002 TYR D 48 ARG 0.005 0.001 ARG N 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 363 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.7989 (t0) cc_final: 0.7636 (m-30) REVERT: B 655 LYS cc_start: 0.7402 (pttm) cc_final: 0.7019 (mmtm) REVERT: D 80 LEU cc_start: 0.6110 (mp) cc_final: 0.5484 (tt) REVERT: F 117 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7716 (mttt) REVERT: G 655 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7580 (mmtm) REVERT: K 99 ASP cc_start: 0.7409 (p0) cc_final: 0.7078 (p0) REVERT: K 114 GLN cc_start: 0.7573 (tt0) cc_final: 0.7008 (tt0) REVERT: L 585 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: L 648 GLU cc_start: 0.7639 (tp30) cc_final: 0.6995 (pt0) REVERT: M 48 MET cc_start: 0.8096 (mtp) cc_final: 0.7687 (mtm) REVERT: N 87 ASP cc_start: 0.7270 (m-30) cc_final: 0.7037 (m-30) outliers start: 58 outliers final: 43 residues processed: 393 average time/residue: 0.3448 time to fit residues: 200.7044 Evaluate side-chains 330 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 287 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 119 GLN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS F 343 GLN G 591 GLN I 54 ASN K 105 HIS K 246 GLN K 362 ASN L 543 ASN L 577 GLN L 591 GLN M 52 ASN M 119 GLN N 41 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20316 Z= 0.326 Angle : 0.724 18.450 27636 Z= 0.368 Chirality : 0.049 0.249 3261 Planarity : 0.005 0.056 3453 Dihedral : 11.385 95.190 3777 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.61 % Rotamer: Outliers : 4.65 % Allowed : 12.86 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2442 helix: -0.46 (0.26), residues: 411 sheet: -0.90 (0.19), residues: 657 loop : -1.46 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 112 HIS 0.021 0.002 HIS H 116 PHE 0.018 0.002 PHE C 64 TYR 0.023 0.002 TYR I 48 ARG 0.008 0.001 ARG K 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 305 time to evaluate : 2.016 Fit side-chains revert: symmetry clash REVERT: A 282 LYS cc_start: 0.7172 (mttp) cc_final: 0.6158 (mttp) REVERT: B 655 LYS cc_start: 0.7369 (pttm) cc_final: 0.7016 (mmtm) REVERT: D 80 LEU cc_start: 0.6118 (mp) cc_final: 0.5503 (tt) REVERT: D 87 ASP cc_start: 0.7100 (m-30) cc_final: 0.6773 (m-30) REVERT: F 95 MET cc_start: 0.8940 (ttp) cc_final: 0.8671 (ttp) REVERT: F 117 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7705 (mttt) REVERT: K 164 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5825 (pm20) REVERT: K 284 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8468 (mt) REVERT: L 585 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: L 647 GLU cc_start: 0.7093 (tt0) cc_final: 0.6853 (tt0) REVERT: L 648 GLU cc_start: 0.7716 (tp30) cc_final: 0.6952 (pt0) REVERT: M 48 MET cc_start: 0.8111 (mtp) cc_final: 0.7886 (mtm) REVERT: N 87 ASP cc_start: 0.7168 (m-30) cc_final: 0.6867 (m-30) outliers start: 99 outliers final: 58 residues processed: 362 average time/residue: 0.3304 time to fit residues: 178.4838 Evaluate side-chains 333 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 273 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 369 MET Chi-restraints excluded: chain L residue 535 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 105 optimal weight: 0.0270 chunk 148 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 113 ASN D 54 ASN G 543 ASN G 616 ASN L 543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20316 Z= 0.187 Angle : 0.638 19.025 27636 Z= 0.322 Chirality : 0.046 0.229 3261 Planarity : 0.004 0.044 3453 Dihedral : 10.217 87.540 3777 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.32 % Favored : 94.43 % Rotamer: Outliers : 3.29 % Allowed : 15.82 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2442 helix: 0.13 (0.27), residues: 390 sheet: -0.71 (0.19), residues: 663 loop : -1.36 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 50 HIS 0.017 0.001 HIS C 116 PHE 0.012 0.001 PHE C 64 TYR 0.019 0.001 TYR D 48 ARG 0.005 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 285 time to evaluate : 2.240 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8860 (ttp) cc_final: 0.8559 (ttp) REVERT: B 655 LYS cc_start: 0.7402 (pttm) cc_final: 0.7109 (mmtm) REVERT: C 48 MET cc_start: 0.7742 (mtp) cc_final: 0.7453 (mtm) REVERT: D 80 LEU cc_start: 0.6097 (mp) cc_final: 0.5539 (tt) REVERT: F 95 MET cc_start: 0.8929 (ttp) cc_final: 0.8695 (ttp) REVERT: F 117 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7692 (mttt) REVERT: L 648 GLU cc_start: 0.7679 (tp30) cc_final: 0.7022 (pt0) REVERT: M 48 MET cc_start: 0.8003 (mtp) cc_final: 0.7681 (mtm) outliers start: 70 outliers final: 53 residues processed: 326 average time/residue: 0.3170 time to fit residues: 156.7384 Evaluate side-chains 324 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 271 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 430 VAL Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 0.1980 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 0.1980 chunk 210 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 ASN N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20316 Z= 0.328 Angle : 0.692 20.018 27636 Z= 0.349 Chirality : 0.048 0.245 3261 Planarity : 0.004 0.045 3453 Dihedral : 10.252 91.658 3777 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.18 % Favored : 93.53 % Rotamer: Outliers : 4.79 % Allowed : 15.77 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2442 helix: 0.10 (0.27), residues: 390 sheet: -0.66 (0.19), residues: 660 loop : -1.43 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 112 HIS 0.008 0.001 HIS C 35 PHE 0.022 0.002 PHE C 64 TYR 0.019 0.002 TYR I 48 ARG 0.006 0.001 ARG G 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 266 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8921 (ttp) cc_final: 0.8571 (ttp) REVERT: A 284 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 655 LYS cc_start: 0.7500 (pttm) cc_final: 0.7260 (mmtm) REVERT: D 87 ASP cc_start: 0.7137 (m-30) cc_final: 0.6800 (m-30) REVERT: F 117 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7753 (mttt) REVERT: F 132 SER cc_start: 0.8262 (t) cc_final: 0.8032 (m) REVERT: G 626 MET cc_start: 0.7148 (ttt) cc_final: 0.6729 (ttt) REVERT: G 648 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7124 (tp30) REVERT: G 655 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7333 (mmtm) REVERT: I 28 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7339 (t70) REVERT: I 87 ASP cc_start: 0.6927 (m-30) cc_final: 0.6635 (m-30) REVERT: K 164 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5930 (pm20) REVERT: K 477 ASP cc_start: 0.7786 (m-30) cc_final: 0.7334 (m-30) REVERT: L 648 GLU cc_start: 0.7708 (tp30) cc_final: 0.7004 (pt0) REVERT: M 48 MET cc_start: 0.7976 (mtp) cc_final: 0.7664 (mtm) outliers start: 102 outliers final: 76 residues processed: 331 average time/residue: 0.3285 time to fit residues: 163.7537 Evaluate side-chains 331 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 252 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 430 VAL Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain L residue 626 MET Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.5980 chunk 211 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 195 optimal weight: 0.0770 chunk 108 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN G 543 ASN H 119 GLN L 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20316 Z= 0.198 Angle : 0.615 19.299 27636 Z= 0.307 Chirality : 0.045 0.221 3261 Planarity : 0.004 0.044 3453 Dihedral : 9.343 84.973 3777 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.12 % Favored : 94.64 % Rotamer: Outliers : 4.41 % Allowed : 16.85 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2442 helix: 0.27 (0.27), residues: 399 sheet: -0.46 (0.20), residues: 630 loop : -1.32 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 112 HIS 0.004 0.001 HIS C 35 PHE 0.018 0.001 PHE C 64 TYR 0.016 0.001 TYR D 48 ARG 0.005 0.001 ARG F 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 278 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8909 (ttp) cc_final: 0.8664 (ttp) REVERT: C 81 MET cc_start: 0.6984 (tmm) cc_final: 0.6710 (ttp) REVERT: D 31 LYS cc_start: 0.6835 (ttmt) cc_final: 0.6509 (tttt) REVERT: D 87 ASP cc_start: 0.7075 (m-30) cc_final: 0.6761 (m-30) REVERT: F 117 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7755 (mttt) REVERT: F 284 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8189 (mt) REVERT: F 424 ILE cc_start: 0.8768 (mm) cc_final: 0.8545 (mm) REVERT: G 626 MET cc_start: 0.7070 (ttt) cc_final: 0.6674 (ttt) REVERT: G 648 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7084 (tp30) REVERT: G 655 LYS cc_start: 0.7661 (tmmt) cc_final: 0.7307 (mmtm) REVERT: I 28 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7263 (t70) REVERT: I 87 ASP cc_start: 0.6864 (m-30) cc_final: 0.6584 (m-30) REVERT: K 359 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5600 (mm) REVERT: L 632 ASP cc_start: 0.7184 (t0) cc_final: 0.6807 (t0) REVERT: L 648 GLU cc_start: 0.7615 (tp30) cc_final: 0.6935 (pt0) REVERT: L 655 LYS cc_start: 0.7753 (tmmt) cc_final: 0.7287 (mmtm) REVERT: M 3 GLN cc_start: 0.7022 (pt0) cc_final: 0.6795 (pt0) outliers start: 94 outliers final: 61 residues processed: 343 average time/residue: 0.3194 time to fit residues: 165.2174 Evaluate side-chains 331 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 267 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN G 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20316 Z= 0.223 Angle : 0.618 18.880 27636 Z= 0.308 Chirality : 0.045 0.224 3261 Planarity : 0.004 0.042 3453 Dihedral : 9.126 84.582 3777 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.98 % Favored : 93.78 % Rotamer: Outliers : 4.41 % Allowed : 16.95 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2442 helix: 0.37 (0.27), residues: 399 sheet: -0.48 (0.20), residues: 624 loop : -1.33 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 112 HIS 0.005 0.001 HIS C 35 PHE 0.021 0.001 PHE C 64 TYR 0.017 0.001 TYR D 48 ARG 0.008 0.001 ARG L 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 268 time to evaluate : 2.213 Fit side-chains revert: symmetry clash REVERT: A 284 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 629 LEU cc_start: 0.8152 (tp) cc_final: 0.7922 (mt) REVERT: D 87 ASP cc_start: 0.7069 (m-30) cc_final: 0.6768 (m-30) REVERT: F 117 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7693 (mttt) REVERT: F 284 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8215 (mt) REVERT: G 626 MET cc_start: 0.7083 (ttt) cc_final: 0.6700 (ttt) REVERT: G 648 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7083 (tp30) REVERT: G 655 LYS cc_start: 0.7807 (tmmt) cc_final: 0.7540 (tppt) REVERT: I 28 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7232 (t70) REVERT: I 87 ASP cc_start: 0.6833 (m-30) cc_final: 0.6550 (m-30) REVERT: K 164 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6008 (pm20) REVERT: K 359 ILE cc_start: 0.5946 (OUTLIER) cc_final: 0.5652 (mm) REVERT: L 626 MET cc_start: 0.7553 (tpp) cc_final: 0.6865 (tpp) REVERT: L 629 LEU cc_start: 0.8250 (tp) cc_final: 0.7963 (mt) REVERT: L 632 ASP cc_start: 0.7170 (t0) cc_final: 0.6923 (t0) REVERT: L 648 GLU cc_start: 0.7619 (tp30) cc_final: 0.6857 (pt0) REVERT: L 655 LYS cc_start: 0.7765 (tmmt) cc_final: 0.7283 (mmtm) REVERT: M 3 GLN cc_start: 0.7014 (pt0) cc_final: 0.6743 (pt0) REVERT: M 48 MET cc_start: 0.8047 (mtp) cc_final: 0.7733 (mtm) REVERT: M 81 MET cc_start: 0.7206 (tpp) cc_final: 0.6922 (tpp) outliers start: 94 outliers final: 68 residues processed: 332 average time/residue: 0.3233 time to fit residues: 162.2987 Evaluate side-chains 335 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 262 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.0370 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN G 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20316 Z= 0.286 Angle : 0.658 23.107 27636 Z= 0.326 Chirality : 0.046 0.233 3261 Planarity : 0.004 0.044 3453 Dihedral : 9.226 85.828 3777 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.61 % Favored : 94.14 % Rotamer: Outliers : 4.27 % Allowed : 17.42 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2442 helix: 0.32 (0.26), residues: 399 sheet: -0.53 (0.21), residues: 618 loop : -1.30 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 50 HIS 0.007 0.001 HIS C 35 PHE 0.022 0.002 PHE C 64 TYR 0.017 0.001 TYR I 48 ARG 0.005 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 268 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 629 LEU cc_start: 0.8040 (tp) cc_final: 0.7680 (mt) REVERT: D 87 ASP cc_start: 0.7080 (m-30) cc_final: 0.6793 (m-30) REVERT: F 117 LYS cc_start: 0.8003 (mmmt) cc_final: 0.7679 (mttt) REVERT: G 585 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7627 (mtm-85) REVERT: G 626 MET cc_start: 0.7123 (ttt) cc_final: 0.6737 (ttt) REVERT: G 648 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7048 (tp30) REVERT: G 655 LYS cc_start: 0.7859 (tmmt) cc_final: 0.7568 (tppt) REVERT: I 28 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7257 (t70) REVERT: I 87 ASP cc_start: 0.6797 (m-30) cc_final: 0.6525 (m-30) REVERT: K 49 LYS cc_start: 0.8365 (mmtm) cc_final: 0.8157 (tppt) REVERT: K 95 MET cc_start: 0.8926 (ttp) cc_final: 0.8696 (ttp) REVERT: K 164 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6021 (pm20) REVERT: L 629 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7995 (mt) REVERT: L 648 GLU cc_start: 0.7618 (tp30) cc_final: 0.6825 (pt0) REVERT: L 655 LYS cc_start: 0.7725 (tmmt) cc_final: 0.7276 (mmtm) REVERT: M 3 GLN cc_start: 0.7057 (pt0) cc_final: 0.6785 (pt0) REVERT: M 48 MET cc_start: 0.8036 (mtp) cc_final: 0.7709 (mtm) REVERT: M 81 MET cc_start: 0.7221 (tpp) cc_final: 0.6871 (tpp) outliers start: 91 outliers final: 72 residues processed: 329 average time/residue: 0.3250 time to fit residues: 161.1197 Evaluate side-chains 338 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 262 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 171 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 206 optimal weight: 0.3980 chunk 217 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN G 543 ASN G 625 ASN K 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20316 Z= 0.192 Angle : 0.615 22.310 27636 Z= 0.306 Chirality : 0.044 0.216 3261 Planarity : 0.004 0.042 3453 Dihedral : 8.735 81.067 3777 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.51 % Rotamer: Outliers : 3.05 % Allowed : 18.92 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2442 helix: 0.49 (0.26), residues: 402 sheet: -0.41 (0.20), residues: 624 loop : -1.29 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 112 HIS 0.003 0.001 HIS C 35 PHE 0.018 0.001 PHE C 64 TYR 0.017 0.001 TYR F 395 ARG 0.008 0.001 ARG K 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 277 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 ILE cc_start: 0.8810 (mm) cc_final: 0.8537 (mm) REVERT: B 629 LEU cc_start: 0.8036 (tp) cc_final: 0.7799 (mt) REVERT: D 87 ASP cc_start: 0.6982 (m-30) cc_final: 0.6704 (m-30) REVERT: F 117 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7675 (mttt) REVERT: F 284 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8178 (mt) REVERT: F 417 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8119 (mm-40) REVERT: G 585 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7492 (mtm-85) REVERT: G 655 LYS cc_start: 0.7875 (tmmt) cc_final: 0.7619 (tppt) REVERT: I 28 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7074 (t70) REVERT: I 87 ASP cc_start: 0.6720 (m-30) cc_final: 0.6436 (m-30) REVERT: K 95 MET cc_start: 0.8924 (ttp) cc_final: 0.8711 (ttp) REVERT: K 164 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5978 (pm20) REVERT: L 626 MET cc_start: 0.7568 (tpp) cc_final: 0.6838 (tpp) REVERT: L 629 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8018 (mt) REVERT: L 647 GLU cc_start: 0.7186 (tt0) cc_final: 0.6957 (tt0) REVERT: L 648 GLU cc_start: 0.7496 (tp30) cc_final: 0.6846 (pt0) REVERT: L 655 LYS cc_start: 0.7678 (tmmt) cc_final: 0.7307 (mmtm) REVERT: M 48 MET cc_start: 0.8004 (mtp) cc_final: 0.7675 (mtm) REVERT: M 81 MET cc_start: 0.7188 (tpp) cc_final: 0.6887 (tpp) outliers start: 65 outliers final: 55 residues processed: 320 average time/residue: 0.3641 time to fit residues: 176.2391 Evaluate side-chains 319 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 260 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 242 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN G 543 ASN G 616 ASN G 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20316 Z= 0.242 Angle : 0.643 22.848 27636 Z= 0.318 Chirality : 0.046 0.234 3261 Planarity : 0.004 0.042 3453 Dihedral : 8.786 81.973 3777 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.53 % Favored : 94.23 % Rotamer: Outliers : 3.47 % Allowed : 18.64 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2442 helix: 0.49 (0.27), residues: 402 sheet: -0.45 (0.20), residues: 624 loop : -1.31 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 479 HIS 0.006 0.001 HIS C 35 PHE 0.022 0.001 PHE C 64 TYR 0.016 0.001 TYR D 48 ARG 0.008 0.001 ARG K 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 263 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8576 (mt) REVERT: A 424 ILE cc_start: 0.8801 (mm) cc_final: 0.8531 (mm) REVERT: B 629 LEU cc_start: 0.8014 (tp) cc_final: 0.7779 (mt) REVERT: F 117 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7674 (mttt) REVERT: G 585 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7544 (mtm-85) REVERT: G 655 LYS cc_start: 0.7831 (tmmt) cc_final: 0.7588 (tppt) REVERT: I 28 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7142 (t70) REVERT: K 164 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5970 (pm20) REVERT: L 626 MET cc_start: 0.7633 (tpp) cc_final: 0.6893 (tpp) REVERT: L 629 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8040 (mt) REVERT: L 648 GLU cc_start: 0.7544 (tp30) cc_final: 0.6843 (pt0) REVERT: L 655 LYS cc_start: 0.7784 (tmmt) cc_final: 0.7423 (tppt) REVERT: M 48 MET cc_start: 0.7993 (mtp) cc_final: 0.7640 (mtm) REVERT: M 81 MET cc_start: 0.7208 (tpp) cc_final: 0.6826 (tpp) outliers start: 74 outliers final: 63 residues processed: 316 average time/residue: 0.3277 time to fit residues: 155.5476 Evaluate side-chains 328 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 261 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 625 ASN Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 193 optimal weight: 0.5980 chunk 80 optimal weight: 0.4980 chunk 198 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 10.0000 chunk 169 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN G 543 ASN G 625 ASN M 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.198720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.162990 restraints weight = 26195.155| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.13 r_work: 0.3821 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20316 Z= 0.192 Angle : 0.615 22.480 27636 Z= 0.305 Chirality : 0.044 0.227 3261 Planarity : 0.004 0.042 3453 Dihedral : 8.474 79.026 3777 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 3.38 % Allowed : 18.92 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2442 helix: 0.62 (0.27), residues: 402 sheet: -0.40 (0.20), residues: 624 loop : -1.28 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 479 HIS 0.003 0.001 HIS C 35 PHE 0.020 0.001 PHE C 64 TYR 0.015 0.001 TYR D 48 ARG 0.008 0.001 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4574.76 seconds wall clock time: 83 minutes 9.46 seconds (4989.46 seconds total)