Starting phenix.real_space_refine on Wed Apr 10 17:03:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/04_2024/8sb4_40290_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/04_2024/8sb4_40290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/04_2024/8sb4_40290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/04_2024/8sb4_40290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/04_2024/8sb4_40290_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/04_2024/8sb4_40290_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 135 5.16 5 C 12525 2.51 5 N 3345 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 167": "OD1" <-> "OD2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K GLU 172": "OE1" <-> "OE2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "K GLU 269": "OE1" <-> "OE2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K GLU 335": "OE1" <-> "OE2" Residue "K TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 107": "OD1" <-> "OD2" Residue "N TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20041 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: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} 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: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "I" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} 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: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "M" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 10.74, per 1000 atoms: 0.54 Number of scatterers: 20041 At special positions: 0 Unit cell: (158.834, 159.9, 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 135 16.00 O 4036 8.00 N 3345 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 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=2.03 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN U 4 " - " MAN U 5 " " 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 " " 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 8 " " 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 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: 9.33 Conformation dependent library (CDL) restraints added in 3.6 seconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4578 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 35 sheets defined 19.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.882A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.157A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) 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 334 through 351 removed outlier: 3.962A pdb=" N ASP A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.562A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.626A pdb=" N TRP B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for '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: 4.653A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.164A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.753A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 61 removed outlier: 4.488A pdb=" N TYR F 61 " --> pdb=" O ALA F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 61' Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.110A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) 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 334 through 351 removed outlier: 3.973A pdb=" N ASP F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.544A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 535 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 573 through 596 removed outlier: 3.545A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.581A pdb=" N TRP G 614 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 615' Processing helix chain 'G' and resid 618 through 624 removed outlier: 3.658A pdb=" N ILE G 622 " --> pdb=" O ASN G 618 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.756A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 636 " --> pdb=" O ASP G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 4.413A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 657 " --> pdb=" O GLN G 653 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA G 662 " --> pdb=" O GLN G 658 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.728A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 61 removed outlier: 4.413A pdb=" N TYR K 61 " --> pdb=" O ALA K 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 61' Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.813A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.190A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) 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 351 removed outlier: 3.973A pdb=" N ASP K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN K 343 " --> pdb=" O ASN K 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS K 351 " --> pdb=" O ILE K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 475 through 481 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 535 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 573 through 596 removed outlier: 3.536A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 removed outlier: 3.803A pdb=" N TRP L 614 " --> pdb=" O ASN L 611 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER L 615 " --> pdb=" O SER L 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 611 through 615' Processing helix chain 'L' and resid 618 through 624 removed outlier: 3.560A pdb=" N ASP L 624 " --> pdb=" O SER L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.722A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 635 " --> pdb=" O TRP L 631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 636 " --> pdb=" O ASP L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 4.099A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN L 651 " --> pdb=" O GLU L 647 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU L 657 " --> pdb=" O GLN L 653 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 662 " --> pdb=" O GLN L 658 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.794A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.263A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (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 Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 176 removed outlier: 6.181A pdb=" N LYS A 168 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A 163 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.622A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.550A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 386 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.551A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 39 removed outlier: 6.599A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 59 current: chain 'C' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.391A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.440A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR G 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.374A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'F' and resid 166 through 176 removed outlier: 6.165A pdb=" N LYS F 168 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR F 163 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.602A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 260 current: chain 'F' and resid 284 through 308 removed outlier: 6.457A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.770A 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 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 386 current: chain 'F' and resid 467 through 470 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.623A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.592A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 20 through 22 Processing sheet with id=AC5, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.506A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.481A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR L 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.204A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'K' and resid 166 through 176 removed outlier: 6.128A pdb=" N LYS K 168 " --> pdb=" O THR K 163 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR K 163 " --> pdb=" O LYS K 168 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS K 170 " --> pdb=" O THR K 161 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.562A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 271 through 273 removed outlier: 6.556A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 316 through 323 current: chain 'K' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 381 through 386 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD4, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.594A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.682A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AD7, first strand: chain 'N' and resid 20 through 23 Processing sheet with id=AD8, first strand: chain 'N' and resid 47 through 50 removed outlier: 6.432A pdb=" N TRP N 37 " --> pdb=" O ILE N 49 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1419 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: 6.86 Time building geometry restraints manager: 9.79 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: 6356 1.35 - 1.49: 5447 1.49 - 1.62: 8481 1.62 - 1.76: 0 1.76 - 1.89: 183 Bond restraints: 20467 Sorted by residual: bond pdb=" N VAL N 60 " pdb=" CA VAL N 60 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.37e+00 bond pdb=" C2 MAN R 5 " pdb=" O2 MAN R 5 " ideal model delta sigma weight residual 1.407 1.467 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" C HIS N 41 " pdb=" N PRO N 42 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.62e+00 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.585 -0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" N VAL D 60 " pdb=" CA VAL D 60 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.50e+00 ... (remaining 20462 not shown) Histogram of bond angle deviations from ideal: 96.10 - 103.70: 239 103.70 - 111.30: 8602 111.30 - 118.90: 8238 118.90 - 126.50: 10355 126.50 - 134.10: 406 Bond angle restraints: 27840 Sorted by residual: angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.10 -11.40 1.80e+00 3.09e-01 4.01e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.65 -10.95 1.80e+00 3.09e-01 3.70e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.16 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C ASN A 403 " pdb=" N SER A 404 " pdb=" CA SER A 404 " ideal model delta sigma weight residual 121.70 131.95 -10.25 1.80e+00 3.09e-01 3.24e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 131.90 -10.20 1.80e+00 3.09e-01 3.21e+01 ... (remaining 27835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 11970 21.59 - 43.18: 781 43.18 - 64.77: 78 64.77 - 86.36: 83 86.36 - 107.94: 38 Dihedral angle restraints: 12950 sinusoidal: 5786 harmonic: 7164 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -173.13 87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS L 598 " pdb=" SG CYS L 598 " pdb=" SG CYS L 604 " pdb=" CB CYS L 604 " ideal model delta sinusoidal sigma weight residual -86.00 -159.15 73.15 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 12947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2690 0.062 - 0.123: 466 0.123 - 0.184: 115 0.184 - 0.246: 8 0.246 - 0.307: 10 Chirality restraints: 3289 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3286 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 75 " -0.062 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO K 76 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO K 76 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 76 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.018 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP F 112 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 585 " -0.236 9.50e-02 1.11e+02 1.06e-01 7.40e+00 pdb=" NE ARG B 585 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 585 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 585 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 585 " -0.004 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 234 2.64 - 3.20: 18054 3.20 - 3.77: 28572 3.77 - 4.33: 41555 4.33 - 4.90: 68057 Nonbonded interactions: 156472 Sorted by model distance: nonbonded pdb=" OG1 THR D 5 " pdb=" OG1 THR D 23 " model vdw 2.071 2.440 nonbonded pdb=" OG1 THR N 5 " pdb=" OG1 THR N 23 " model vdw 2.073 2.440 nonbonded pdb=" OG1 THR I 5 " pdb=" OG1 THR I 23 " model vdw 2.090 2.440 nonbonded pdb=" O THR M 30 " pdb=" OG SER M 54 " model vdw 2.098 2.440 nonbonded pdb=" OG1 THR F 163 " pdb=" OE1 GLU F 164 " model vdw 2.117 2.440 ... (remaining 156467 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' and (resid 2 or resid 5 through 9)) selection = (chain 'R' and (resid 1 or resid 4 through 8)) selection = (chain 'V' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.700 Check model and map are aligned: 0.280 Set scattering table: 0.200 Process input model: 54.860 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 0.084 20467 Z= 0.364 Angle : 0.933 11.405 27840 Z= 0.490 Chirality : 0.054 0.307 3289 Planarity : 0.006 0.106 3480 Dihedral : 16.323 107.944 8246 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.83 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.55 (0.16), residues: 2466 helix: -1.74 (0.24), residues: 354 sheet: -0.26 (0.19), residues: 660 loop : -1.20 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 112 HIS 0.008 0.002 HIS I 41 PHE 0.017 0.002 PHE K 391 TYR 0.020 0.002 TYR D 51 ARG 0.016 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6775 (m-30) cc_final: 0.6556 (m-30) REVERT: A 121 LYS cc_start: 0.7017 (ptpt) cc_final: 0.6689 (ttmm) REVERT: B 535 MET cc_start: 0.8113 (mtt) cc_final: 0.7418 (mtt) REVERT: B 632 ASP cc_start: 0.7977 (t70) cc_final: 0.7567 (t0) REVERT: B 661 LEU cc_start: 0.8854 (tp) cc_final: 0.8465 (mt) REVERT: C 7 SER cc_start: 0.7703 (p) cc_final: 0.7294 (p) REVERT: C 21 SER cc_start: 0.7955 (p) cc_final: 0.7623 (t) REVERT: C 43 GLN cc_start: 0.7377 (tp40) cc_final: 0.6783 (mp10) REVERT: C 84 ASN cc_start: 0.8031 (t0) cc_final: 0.7798 (t0) REVERT: D 92 SER cc_start: 0.8913 (p) cc_final: 0.8694 (p) REVERT: F 54 CYS cc_start: 0.5359 (p) cc_final: 0.5133 (p) REVERT: F 103 GLN cc_start: 0.7654 (mt0) cc_final: 0.7146 (tm-30) REVERT: F 442 ASN cc_start: 0.8083 (p0) cc_final: 0.7867 (p0) REVERT: G 604 CYS cc_start: 0.6761 (t) cc_final: 0.6492 (t) REVERT: G 632 ASP cc_start: 0.7831 (t70) cc_final: 0.7434 (t0) REVERT: G 660 LEU cc_start: 0.7691 (mt) cc_final: 0.7289 (tt) REVERT: G 661 LEU cc_start: 0.8850 (tp) cc_final: 0.8439 (mt) REVERT: H 13 LYS cc_start: 0.7485 (mmpt) cc_final: 0.7262 (mmtt) REVERT: H 43 GLN cc_start: 0.7495 (tp40) cc_final: 0.6727 (mp10) REVERT: H 84 ASN cc_start: 0.8452 (t0) cc_final: 0.8185 (t0) REVERT: I 25 THR cc_start: 0.8086 (t) cc_final: 0.7589 (m) REVERT: I 36 SER cc_start: 0.8859 (m) cc_final: 0.8656 (t) REVERT: I 38 TYR cc_start: 0.8087 (m-80) cc_final: 0.7114 (m-80) REVERT: I 93 TYR cc_start: 0.8918 (t80) cc_final: 0.8391 (t80) REVERT: K 162 THR cc_start: 0.8345 (m) cc_final: 0.8053 (p) REVERT: L 608 VAL cc_start: 0.8485 (t) cc_final: 0.7955 (t) REVERT: L 634 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7844 (mt-10) REVERT: M 122 LEU cc_start: 0.7846 (mt) cc_final: 0.7435 (mp) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.3483 time to fit residues: 331.3692 Evaluate side-chains 420 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 478 ASN B 590 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 6 GLN C 43 GLN D 40 GLN F 287 HIS F 352 HIS G 575 GLN G 630 GLN H 43 GLN H 113 ASN K 287 HIS K 352 HIS L 630 GLN M 6 GLN M 39 GLN M 43 GLN N 40 GLN N 41 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20467 Z= 0.397 Angle : 0.789 9.966 27840 Z= 0.405 Chirality : 0.051 0.361 3289 Planarity : 0.005 0.062 3480 Dihedral : 11.525 75.166 3794 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.99 % Favored : 94.65 % Rotamer: Outliers : 2.65 % Allowed : 11.70 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.48 (0.16), residues: 2466 helix: -1.63 (0.24), residues: 393 sheet: -0.29 (0.18), residues: 708 loop : -1.12 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 35 HIS 0.007 0.002 HIS K 330 PHE 0.020 0.003 PHE F 376 TYR 0.029 0.002 TYR D 93 ARG 0.008 0.001 ARG L 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 432 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7366 (ptpt) cc_final: 0.7093 (ttmm) REVERT: A 207 LYS cc_start: 0.7244 (tmtt) cc_final: 0.6649 (tmtt) REVERT: A 211 GLU cc_start: 0.8112 (tt0) cc_final: 0.7762 (pt0) REVERT: B 632 ASP cc_start: 0.8211 (t0) cc_final: 0.7686 (t0) REVERT: B 661 LEU cc_start: 0.8712 (tp) cc_final: 0.8405 (mt) REVERT: C 7 SER cc_start: 0.7922 (p) cc_final: 0.7647 (p) REVERT: C 13 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6862 (mmmt) REVERT: C 21 SER cc_start: 0.8151 (p) cc_final: 0.7874 (t) REVERT: C 38 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7655 (ttp80) REVERT: C 43 GLN cc_start: 0.7133 (tp-100) cc_final: 0.6620 (mp10) REVERT: D 23 THR cc_start: 0.7230 (p) cc_final: 0.6976 (t) REVERT: F 54 CYS cc_start: 0.5477 (p) cc_final: 0.5202 (p) REVERT: F 103 GLN cc_start: 0.7552 (mt0) cc_final: 0.7166 (tm-30) REVERT: F 164 GLU cc_start: 0.7462 (pm20) cc_final: 0.7174 (pm20) REVERT: F 343 GLN cc_start: 0.7687 (mt0) cc_final: 0.7284 (pt0) REVERT: G 632 ASP cc_start: 0.8083 (t70) cc_final: 0.7650 (t0) REVERT: G 659 ASP cc_start: 0.8234 (m-30) cc_final: 0.7859 (t70) REVERT: G 661 LEU cc_start: 0.8897 (tp) cc_final: 0.8452 (mt) REVERT: H 43 GLN cc_start: 0.7529 (tp-100) cc_final: 0.7218 (mp10) REVERT: H 81 MET cc_start: 0.7689 (tmm) cc_final: 0.7288 (tmm) REVERT: H 84 ASN cc_start: 0.8288 (t0) cc_final: 0.8075 (t0) REVERT: I 36 SER cc_start: 0.9058 (m) cc_final: 0.8684 (t) REVERT: I 38 TYR cc_start: 0.8174 (m-80) cc_final: 0.7502 (m-80) REVERT: I 107 LEU cc_start: 0.7042 (tp) cc_final: 0.6794 (tp) REVERT: K 103 GLN cc_start: 0.7739 (mt0) cc_final: 0.7489 (tm-30) REVERT: K 116 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8094 (mp) REVERT: K 162 THR cc_start: 0.8417 (m) cc_final: 0.8201 (p) REVERT: K 207 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7632 (tttp) REVERT: L 584 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7860 (mt-10) REVERT: M 70 MET cc_start: 0.8843 (mtm) cc_final: 0.8589 (mtm) outliers start: 57 outliers final: 32 residues processed: 457 average time/residue: 0.3325 time to fit residues: 230.6461 Evaluate side-chains 400 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 366 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 283 ILE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain L residue 606 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 223 optimal weight: 0.0370 chunk 241 optimal weight: 40.0000 chunk 199 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN B 630 GLN F 114 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 658 GLN N 40 GLN N 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20467 Z= 0.188 Angle : 0.643 10.254 27840 Z= 0.328 Chirality : 0.045 0.353 3289 Planarity : 0.004 0.057 3480 Dihedral : 9.772 67.803 3794 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.54 % Favored : 95.09 % Rotamer: Outliers : 2.32 % Allowed : 15.32 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.05 (0.16), residues: 2466 helix: -1.13 (0.25), residues: 393 sheet: -0.02 (0.19), residues: 708 loop : -0.89 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 50 HIS 0.003 0.001 HIS K 374 PHE 0.013 0.002 PHE A 391 TYR 0.024 0.002 TYR N 51 ARG 0.006 0.001 ARG N 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 401 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7255 (tmtt) cc_final: 0.6603 (tmtt) REVERT: A 211 GLU cc_start: 0.7944 (tt0) cc_final: 0.7635 (pt0) REVERT: B 632 ASP cc_start: 0.8142 (t70) cc_final: 0.7594 (t0) REVERT: B 637 ASN cc_start: 0.6242 (OUTLIER) cc_final: 0.5737 (p0) REVERT: B 638 TYR cc_start: 0.7450 (m-80) cc_final: 0.7123 (m-80) REVERT: B 647 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6811 (mp0) REVERT: B 661 LEU cc_start: 0.8850 (tp) cc_final: 0.8396 (mt) REVERT: C 21 SER cc_start: 0.8248 (p) cc_final: 0.7951 (t) REVERT: C 38 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7724 (ttp80) REVERT: D 23 THR cc_start: 0.7105 (p) cc_final: 0.6841 (t) REVERT: F 57 ASP cc_start: 0.7125 (t0) cc_final: 0.6733 (p0) REVERT: F 164 GLU cc_start: 0.7468 (pm20) cc_final: 0.7261 (pm20) REVERT: G 632 ASP cc_start: 0.8009 (t70) cc_final: 0.7575 (t0) REVERT: G 661 LEU cc_start: 0.8787 (tp) cc_final: 0.8550 (mt) REVERT: H 43 GLN cc_start: 0.7459 (tp-100) cc_final: 0.7202 (mp10) REVERT: H 81 MET cc_start: 0.7490 (tmm) cc_final: 0.7115 (tmm) REVERT: I 20 ILE cc_start: 0.6921 (mt) cc_final: 0.6718 (mt) REVERT: I 36 SER cc_start: 0.9040 (m) cc_final: 0.8653 (t) REVERT: I 38 TYR cc_start: 0.8149 (m-80) cc_final: 0.7735 (m-80) REVERT: I 68 LYS cc_start: 0.7314 (tttt) cc_final: 0.7027 (tttp) REVERT: I 106 LYS cc_start: 0.7529 (tppt) cc_final: 0.7279 (tppt) REVERT: K 107 ASP cc_start: 0.7727 (t0) cc_final: 0.7504 (t0) REVERT: K 162 THR cc_start: 0.8336 (m) cc_final: 0.8134 (p) REVERT: K 207 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7605 (tttp) REVERT: L 584 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7784 (mt-10) REVERT: L 607 ASN cc_start: 0.8944 (t0) cc_final: 0.8482 (m-40) REVERT: L 632 ASP cc_start: 0.8214 (t70) cc_final: 0.7723 (t0) REVERT: M 21 SER cc_start: 0.7957 (p) cc_final: 0.7591 (t) REVERT: M 38 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7909 (ttp80) REVERT: M 70 MET cc_start: 0.8894 (mtm) cc_final: 0.8533 (mtm) outliers start: 50 outliers final: 26 residues processed: 427 average time/residue: 0.3234 time to fit residues: 209.7692 Evaluate side-chains 394 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 366 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 6.9990 chunk 168 optimal weight: 0.0980 chunk 116 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 343 GLN A 362 ASN A 478 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 HIS K 362 ASN L 590 GLN N 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20467 Z= 0.394 Angle : 0.725 9.947 27840 Z= 0.369 Chirality : 0.048 0.331 3289 Planarity : 0.005 0.057 3480 Dihedral : 9.053 66.848 3794 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.76 % Favored : 93.88 % Rotamer: Outliers : 4.04 % Allowed : 16.57 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.18 (0.16), residues: 2466 helix: -1.09 (0.26), residues: 393 sheet: -0.02 (0.20), residues: 657 loop : -1.05 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.006 0.001 HIS K 330 PHE 0.018 0.002 PHE F 376 TYR 0.023 0.002 TYR N 51 ARG 0.006 0.001 ARG F 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 382 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7624 (t0) cc_final: 0.7001 (p0) REVERT: A 211 GLU cc_start: 0.7915 (tt0) cc_final: 0.7677 (pt0) REVERT: B 632 ASP cc_start: 0.8251 (t0) cc_final: 0.7708 (t0) REVERT: B 638 TYR cc_start: 0.7562 (m-80) cc_final: 0.7159 (m-10) REVERT: B 661 LEU cc_start: 0.8844 (tp) cc_final: 0.8357 (mt) REVERT: C 93 MET cc_start: 0.6486 (tpp) cc_final: 0.6282 (tpp) REVERT: D 23 THR cc_start: 0.7075 (p) cc_final: 0.6798 (t) REVERT: F 57 ASP cc_start: 0.7428 (t0) cc_final: 0.7075 (p0) REVERT: G 632 ASP cc_start: 0.8163 (t70) cc_final: 0.7710 (t0) REVERT: H 38 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8177 (ttp80) REVERT: H 43 GLN cc_start: 0.7520 (tp-100) cc_final: 0.7139 (mp10) REVERT: H 81 MET cc_start: 0.7592 (tmm) cc_final: 0.7197 (tmm) REVERT: I 23 THR cc_start: 0.7302 (p) cc_final: 0.6997 (t) REVERT: I 36 SER cc_start: 0.8995 (m) cc_final: 0.8540 (t) REVERT: I 68 LYS cc_start: 0.7318 (tttt) cc_final: 0.7082 (tttp) REVERT: K 57 ASP cc_start: 0.7608 (t0) cc_final: 0.6932 (p0) REVERT: K 162 THR cc_start: 0.8556 (m) cc_final: 0.8295 (p) REVERT: K 207 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7661 (tttp) REVERT: L 584 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7679 (mt-10) REVERT: L 607 ASN cc_start: 0.8967 (t0) cc_final: 0.8515 (m-40) outliers start: 87 outliers final: 67 residues processed: 436 average time/residue: 0.3255 time to fit residues: 216.8132 Evaluate side-chains 415 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 347 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 425 ASN Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 637 ASN Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 3 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 213 optimal weight: 0.0010 chunk 60 optimal weight: 4.9990 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN B 540 GLN B 616 ASN G 540 GLN G 543 ASN G 656 ASN I 6 GLN N 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20467 Z= 0.182 Angle : 0.615 10.305 27840 Z= 0.312 Chirality : 0.045 0.345 3289 Planarity : 0.004 0.052 3480 Dihedral : 8.110 58.516 3794 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.97 % Favored : 95.70 % Rotamer: Outliers : 2.92 % Allowed : 18.01 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.98 (0.16), residues: 2466 helix: -0.90 (0.26), residues: 393 sheet: 0.16 (0.20), residues: 654 loop : -0.96 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.003 0.001 HIS K 374 PHE 0.012 0.001 PHE A 210 TYR 0.025 0.001 TYR N 51 ARG 0.008 0.000 ARG L 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 365 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7578 (t0) cc_final: 0.6979 (p0) REVERT: A 211 GLU cc_start: 0.7948 (tt0) cc_final: 0.7687 (pt0) REVERT: B 632 ASP cc_start: 0.8232 (t70) cc_final: 0.7673 (t0) REVERT: B 638 TYR cc_start: 0.7589 (m-80) cc_final: 0.6953 (m-10) REVERT: B 661 LEU cc_start: 0.8686 (tp) cc_final: 0.8230 (mt) REVERT: C 38 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7738 (ttp80) REVERT: F 57 ASP cc_start: 0.7441 (t0) cc_final: 0.6819 (p0) REVERT: G 591 GLN cc_start: 0.8220 (tt0) cc_final: 0.7983 (tt0) REVERT: G 632 ASP cc_start: 0.8075 (t70) cc_final: 0.7640 (t0) REVERT: H 13 LYS cc_start: 0.8434 (pptt) cc_final: 0.7595 (mmmt) REVERT: H 73 ASP cc_start: 0.8303 (m-30) cc_final: 0.7997 (m-30) REVERT: H 81 MET cc_start: 0.7593 (tmm) cc_final: 0.7191 (tmm) REVERT: I 20 ILE cc_start: 0.7075 (mt) cc_final: 0.6731 (mt) REVERT: I 23 THR cc_start: 0.7413 (p) cc_final: 0.7119 (t) REVERT: I 36 SER cc_start: 0.9065 (m) cc_final: 0.8617 (t) REVERT: I 68 LYS cc_start: 0.7299 (tttt) cc_final: 0.7029 (tttp) REVERT: I 106 LYS cc_start: 0.8112 (tppt) cc_final: 0.7831 (tppt) REVERT: K 57 ASP cc_start: 0.7482 (t0) cc_final: 0.6829 (p0) REVERT: K 162 THR cc_start: 0.8475 (m) cc_final: 0.8236 (p) REVERT: K 207 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7585 (tptp) REVERT: L 584 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7822 (mt-10) REVERT: L 607 ASN cc_start: 0.8763 (t0) cc_final: 0.8332 (m-40) REVERT: L 629 LEU cc_start: 0.7280 (tt) cc_final: 0.6916 (mt) REVERT: M 70 MET cc_start: 0.9001 (mtm) cc_final: 0.8627 (mtm) outliers start: 63 outliers final: 47 residues processed: 405 average time/residue: 0.3338 time to fit residues: 204.7192 Evaluate side-chains 391 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 343 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 110 optimal weight: 0.0000 chunk 19 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 124 optimal weight: 0.9980 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN D 62 ASN I 6 GLN ** L 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20467 Z= 0.234 Angle : 0.622 11.821 27840 Z= 0.315 Chirality : 0.045 0.339 3289 Planarity : 0.004 0.050 3480 Dihedral : 7.722 56.413 3794 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.99 % Favored : 94.69 % Rotamer: Outliers : 3.20 % Allowed : 18.80 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.96 (0.16), residues: 2466 helix: -0.83 (0.26), residues: 393 sheet: 0.19 (0.20), residues: 657 loop : -0.97 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 628 HIS 0.004 0.001 HIS F 330 PHE 0.011 0.001 PHE K 93 TYR 0.026 0.002 TYR N 51 ARG 0.009 0.001 ARG M 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 356 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7537 (t0) cc_final: 0.6992 (p0) REVERT: A 211 GLU cc_start: 0.7843 (tt0) cc_final: 0.7518 (pt0) REVERT: B 632 ASP cc_start: 0.8251 (t70) cc_final: 0.7692 (t0) REVERT: B 638 TYR cc_start: 0.7601 (m-80) cc_final: 0.7317 (m-10) REVERT: B 659 ASP cc_start: 0.8268 (m-30) cc_final: 0.7832 (t70) REVERT: B 661 LEU cc_start: 0.8725 (tp) cc_final: 0.8285 (mt) REVERT: C 38 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7805 (ttp80) REVERT: D 63 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5694 (ptm160) REVERT: D 106 LYS cc_start: 0.7766 (tppt) cc_final: 0.7544 (tppt) REVERT: F 57 ASP cc_start: 0.7443 (t0) cc_final: 0.6822 (p0) REVERT: F 207 LYS cc_start: 0.7770 (tttp) cc_final: 0.7526 (tttp) REVERT: G 535 MET cc_start: 0.8098 (tpp) cc_final: 0.7760 (tpp) REVERT: G 632 ASP cc_start: 0.8067 (t70) cc_final: 0.7615 (t0) REVERT: H 13 LYS cc_start: 0.8430 (pptt) cc_final: 0.7616 (mmmt) REVERT: H 43 GLN cc_start: 0.7686 (mp10) cc_final: 0.7388 (mp10) REVERT: H 73 ASP cc_start: 0.8301 (m-30) cc_final: 0.8002 (m-30) REVERT: H 81 MET cc_start: 0.7584 (tmm) cc_final: 0.7206 (tmm) REVERT: I 20 ILE cc_start: 0.6960 (mt) cc_final: 0.6727 (mt) REVERT: I 23 THR cc_start: 0.7542 (p) cc_final: 0.7253 (t) REVERT: I 36 SER cc_start: 0.8976 (m) cc_final: 0.8566 (t) REVERT: I 42 PRO cc_start: 0.8501 (Cg_exo) cc_final: 0.8291 (Cg_endo) REVERT: I 68 LYS cc_start: 0.7287 (tttt) cc_final: 0.6972 (tttp) REVERT: K 57 ASP cc_start: 0.7514 (t0) cc_final: 0.6839 (p0) REVERT: K 162 THR cc_start: 0.8522 (m) cc_final: 0.8280 (p) REVERT: K 207 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7714 (tptp) REVERT: L 584 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7870 (mt-10) REVERT: L 607 ASN cc_start: 0.8770 (t0) cc_final: 0.8463 (m-40) REVERT: L 629 LEU cc_start: 0.7268 (tt) cc_final: 0.6977 (mt) REVERT: M 70 MET cc_start: 0.9044 (mtm) cc_final: 0.8598 (mtm) REVERT: N 63 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6810 (mmm-85) outliers start: 69 outliers final: 55 residues processed: 399 average time/residue: 0.3191 time to fit residues: 195.1767 Evaluate side-chains 395 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 338 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 540 GLN Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 200 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 chunk 237 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN ** L 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20467 Z= 0.190 Angle : 0.606 11.827 27840 Z= 0.305 Chirality : 0.044 0.342 3289 Planarity : 0.004 0.052 3480 Dihedral : 7.322 54.488 3794 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.46 % Favored : 95.21 % Rotamer: Outliers : 3.11 % Allowed : 19.55 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.90 (0.16), residues: 2466 helix: -0.73 (0.26), residues: 393 sheet: 0.30 (0.21), residues: 621 loop : -0.95 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 628 HIS 0.003 0.001 HIS M 35 PHE 0.009 0.001 PHE K 93 TYR 0.026 0.001 TYR N 51 ARG 0.009 0.001 ARG G 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 352 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7485 (t0) cc_final: 0.6926 (p0) REVERT: A 211 GLU cc_start: 0.7847 (tt0) cc_final: 0.7536 (pt0) REVERT: B 629 LEU cc_start: 0.7712 (tp) cc_final: 0.7367 (mt) REVERT: B 632 ASP cc_start: 0.8249 (t70) cc_final: 0.7739 (t0) REVERT: B 638 TYR cc_start: 0.7653 (m-80) cc_final: 0.7311 (m-80) REVERT: B 659 ASP cc_start: 0.8201 (m-30) cc_final: 0.7776 (t70) REVERT: B 661 LEU cc_start: 0.8775 (tp) cc_final: 0.8280 (mt) REVERT: F 57 ASP cc_start: 0.7583 (t0) cc_final: 0.6907 (p0) REVERT: F 207 LYS cc_start: 0.7806 (tttp) cc_final: 0.7570 (tttp) REVERT: G 535 MET cc_start: 0.8076 (tpp) cc_final: 0.7729 (tpp) REVERT: G 591 GLN cc_start: 0.8182 (tt0) cc_final: 0.7955 (tt0) REVERT: G 632 ASP cc_start: 0.8037 (t70) cc_final: 0.7584 (t0) REVERT: H 13 LYS cc_start: 0.8453 (pptt) cc_final: 0.7697 (mmmt) REVERT: H 43 GLN cc_start: 0.7699 (mp10) cc_final: 0.7429 (mp10) REVERT: H 73 ASP cc_start: 0.8254 (m-30) cc_final: 0.7973 (m-30) REVERT: H 81 MET cc_start: 0.7661 (tmm) cc_final: 0.7238 (tmm) REVERT: I 20 ILE cc_start: 0.6863 (mt) cc_final: 0.6630 (mt) REVERT: I 36 SER cc_start: 0.8963 (m) cc_final: 0.8585 (t) REVERT: I 42 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8294 (Cg_endo) REVERT: I 106 LYS cc_start: 0.8271 (tppt) cc_final: 0.7983 (tppt) REVERT: K 57 ASP cc_start: 0.7389 (t0) cc_final: 0.6736 (p0) REVERT: K 162 THR cc_start: 0.8494 (m) cc_final: 0.8258 (p) REVERT: K 207 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7700 (tptp) REVERT: L 584 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7853 (mt-10) REVERT: L 607 ASN cc_start: 0.8746 (t0) cc_final: 0.8461 (m-40) REVERT: M 70 MET cc_start: 0.9027 (mtm) cc_final: 0.8581 (mtm) outliers start: 67 outliers final: 55 residues processed: 395 average time/residue: 0.3274 time to fit residues: 197.3946 Evaluate side-chains 395 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 340 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 0.4980 chunk 71 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 150 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 overall best weight: 1.1278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN G 616 ASN I 6 GLN ** L 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20467 Z= 0.164 Angle : 0.591 11.370 27840 Z= 0.298 Chirality : 0.044 0.341 3289 Planarity : 0.004 0.047 3480 Dihedral : 6.776 53.818 3794 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.46 % Favored : 95.21 % Rotamer: Outliers : 3.02 % Allowed : 19.59 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.77 (0.16), residues: 2466 helix: -0.51 (0.26), residues: 393 sheet: 0.39 (0.21), residues: 621 loop : -0.92 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 628 HIS 0.003 0.001 HIS M 35 PHE 0.008 0.001 PHE F 317 TYR 0.025 0.001 TYR N 51 ARG 0.008 0.001 ARG G 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 374 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7392 (t0) cc_final: 0.6825 (p0) REVERT: A 211 GLU cc_start: 0.7803 (tt0) cc_final: 0.7527 (pt0) REVERT: B 579 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7878 (ttp-170) REVERT: B 629 LEU cc_start: 0.7549 (tp) cc_final: 0.7273 (mt) REVERT: B 632 ASP cc_start: 0.8155 (t70) cc_final: 0.7641 (t0) REVERT: B 659 ASP cc_start: 0.8163 (m-30) cc_final: 0.7745 (t70) REVERT: B 661 LEU cc_start: 0.8707 (tp) cc_final: 0.8225 (mt) REVERT: C 48 MET cc_start: 0.7978 (mtp) cc_final: 0.7658 (mtm) REVERT: D 63 ARG cc_start: 0.6398 (OUTLIER) cc_final: 0.5851 (ptm-80) REVERT: F 57 ASP cc_start: 0.7514 (t0) cc_final: 0.6900 (p0) REVERT: F 207 LYS cc_start: 0.8014 (tttp) cc_final: 0.7725 (tptp) REVERT: F 283 ILE cc_start: 0.8738 (mt) cc_final: 0.8489 (tt) REVERT: G 535 MET cc_start: 0.8028 (tpp) cc_final: 0.7660 (tpp) REVERT: G 591 GLN cc_start: 0.8118 (tt0) cc_final: 0.7894 (tt0) REVERT: G 632 ASP cc_start: 0.7990 (t70) cc_final: 0.7567 (t0) REVERT: H 13 LYS cc_start: 0.8403 (pptt) cc_final: 0.7699 (mmmt) REVERT: H 73 ASP cc_start: 0.8287 (m-30) cc_final: 0.7988 (m-30) REVERT: H 81 MET cc_start: 0.7633 (tmm) cc_final: 0.7180 (tmm) REVERT: I 20 ILE cc_start: 0.6795 (mt) cc_final: 0.6572 (mt) REVERT: I 36 SER cc_start: 0.8951 (m) cc_final: 0.8554 (t) REVERT: I 42 PRO cc_start: 0.8548 (Cg_exo) cc_final: 0.8326 (Cg_endo) REVERT: I 106 LYS cc_start: 0.8268 (tppt) cc_final: 0.8031 (tppt) REVERT: K 57 ASP cc_start: 0.7286 (t0) cc_final: 0.6689 (p0) REVERT: K 162 THR cc_start: 0.8448 (m) cc_final: 0.8225 (p) REVERT: K 207 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7616 (tptp) REVERT: K 276 ASN cc_start: 0.6373 (t0) cc_final: 0.5974 (p0) REVERT: L 584 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: L 607 ASN cc_start: 0.8716 (t0) cc_final: 0.8446 (m-40) REVERT: M 70 MET cc_start: 0.9010 (mtm) cc_final: 0.8544 (mtm) outliers start: 65 outliers final: 51 residues processed: 416 average time/residue: 0.3268 time to fit residues: 208.5253 Evaluate side-chains 403 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 350 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 39 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 96 optimal weight: 0.0570 chunk 173 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN F 463 ASN I 6 GLN ** L 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20467 Z= 0.180 Angle : 0.604 11.594 27840 Z= 0.304 Chirality : 0.044 0.339 3289 Planarity : 0.004 0.045 3480 Dihedral : 6.532 54.326 3794 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.50 % Favored : 95.17 % Rotamer: Outliers : 2.97 % Allowed : 19.87 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.70 (0.16), residues: 2466 helix: -0.36 (0.26), residues: 393 sheet: 0.42 (0.21), residues: 624 loop : -0.88 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 628 HIS 0.004 0.001 HIS C 35 PHE 0.008 0.001 PHE F 391 TYR 0.024 0.001 TYR N 51 ARG 0.005 0.000 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 354 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7448 (t0) cc_final: 0.6799 (p0) REVERT: A 211 GLU cc_start: 0.7877 (tt0) cc_final: 0.7511 (pt0) REVERT: B 579 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.7854 (ttp-170) REVERT: B 629 LEU cc_start: 0.7693 (tp) cc_final: 0.7348 (mt) REVERT: B 632 ASP cc_start: 0.8199 (t70) cc_final: 0.7701 (t0) REVERT: B 638 TYR cc_start: 0.7560 (m-10) cc_final: 0.7297 (m-10) REVERT: B 659 ASP cc_start: 0.8137 (m-30) cc_final: 0.7736 (t70) REVERT: B 661 LEU cc_start: 0.8727 (tp) cc_final: 0.8159 (mt) REVERT: C 70 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8592 (mtt) REVERT: D 42 PRO cc_start: 0.8582 (Cg_exo) cc_final: 0.8266 (Cg_endo) REVERT: F 207 LYS cc_start: 0.8086 (tttp) cc_final: 0.7751 (tptp) REVERT: F 283 ILE cc_start: 0.8763 (mt) cc_final: 0.8518 (tt) REVERT: G 535 MET cc_start: 0.8045 (tpp) cc_final: 0.7680 (tpp) REVERT: G 591 GLN cc_start: 0.8154 (tt0) cc_final: 0.7901 (tt0) REVERT: G 629 LEU cc_start: 0.7453 (tt) cc_final: 0.7107 (mt) REVERT: H 13 LYS cc_start: 0.8375 (pptt) cc_final: 0.7711 (mmmt) REVERT: H 73 ASP cc_start: 0.8364 (m-30) cc_final: 0.8062 (m-30) REVERT: H 81 MET cc_start: 0.7475 (tmm) cc_final: 0.7172 (tmm) REVERT: I 20 ILE cc_start: 0.6743 (mt) cc_final: 0.6492 (mt) REVERT: I 36 SER cc_start: 0.8910 (m) cc_final: 0.8544 (t) REVERT: I 42 PRO cc_start: 0.8543 (Cg_exo) cc_final: 0.8328 (Cg_endo) REVERT: K 57 ASP cc_start: 0.7285 (t0) cc_final: 0.6758 (p0) REVERT: K 162 THR cc_start: 0.8479 (m) cc_final: 0.8247 (p) REVERT: K 207 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7607 (tptp) REVERT: K 276 ASN cc_start: 0.6453 (t0) cc_final: 0.5914 (p0) REVERT: L 584 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: L 607 ASN cc_start: 0.8723 (t0) cc_final: 0.8462 (m-40) REVERT: M 70 MET cc_start: 0.9016 (mtm) cc_final: 0.8553 (mtm) outliers start: 64 outliers final: 54 residues processed: 395 average time/residue: 0.3332 time to fit residues: 201.1727 Evaluate side-chains 396 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 340 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 GLN I 6 GLN L 543 ASN ** L 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 20467 Z= 0.272 Angle : 0.766 59.185 27840 Z= 0.426 Chirality : 0.045 0.341 3289 Planarity : 0.004 0.047 3480 Dihedral : 6.540 54.344 3794 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.62 % Favored : 95.05 % Rotamer: Outliers : 2.88 % Allowed : 19.78 % Favored : 77.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % 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: -0.70 (0.16), residues: 2466 helix: -0.38 (0.26), residues: 393 sheet: 0.44 (0.21), residues: 621 loop : -0.89 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 614 HIS 0.004 0.001 HIS C 35 PHE 0.009 0.001 PHE F 317 TYR 0.046 0.002 TYR F 361 ARG 0.005 0.000 ARG B 579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 342 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7443 (t0) cc_final: 0.6805 (p0) REVERT: A 211 GLU cc_start: 0.7883 (tt0) cc_final: 0.7533 (pt0) REVERT: B 579 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7872 (ttp-170) REVERT: B 629 LEU cc_start: 0.7689 (tp) cc_final: 0.7354 (mt) REVERT: B 632 ASP cc_start: 0.8211 (t70) cc_final: 0.7699 (t0) REVERT: B 638 TYR cc_start: 0.7564 (m-10) cc_final: 0.7303 (m-10) REVERT: B 659 ASP cc_start: 0.8141 (m-30) cc_final: 0.7739 (t70) REVERT: B 661 LEU cc_start: 0.8627 (tp) cc_final: 0.8140 (mt) REVERT: D 42 PRO cc_start: 0.8587 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: F 207 LYS cc_start: 0.8095 (tttp) cc_final: 0.7755 (tptp) REVERT: F 283 ILE cc_start: 0.8780 (mt) cc_final: 0.8521 (tt) REVERT: G 535 MET cc_start: 0.8060 (tpp) cc_final: 0.7684 (tpp) REVERT: G 591 GLN cc_start: 0.8134 (tt0) cc_final: 0.7889 (tt0) REVERT: G 629 LEU cc_start: 0.7487 (tt) cc_final: 0.7116 (mt) REVERT: H 13 LYS cc_start: 0.8377 (pptt) cc_final: 0.7713 (mmmt) REVERT: H 73 ASP cc_start: 0.8372 (m-30) cc_final: 0.8063 (m-30) REVERT: H 81 MET cc_start: 0.7557 (tmm) cc_final: 0.7177 (tmm) REVERT: I 20 ILE cc_start: 0.6742 (mt) cc_final: 0.6498 (mt) REVERT: I 36 SER cc_start: 0.8911 (m) cc_final: 0.8550 (t) REVERT: I 42 PRO cc_start: 0.8535 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: K 57 ASP cc_start: 0.7289 (t0) cc_final: 0.6757 (p0) REVERT: K 162 THR cc_start: 0.8447 (m) cc_final: 0.8209 (p) REVERT: K 207 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7608 (tptp) REVERT: K 276 ASN cc_start: 0.6461 (t0) cc_final: 0.5919 (p0) REVERT: L 584 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: L 607 ASN cc_start: 0.8728 (t0) cc_final: 0.8462 (m-40) REVERT: M 70 MET cc_start: 0.9020 (mtm) cc_final: 0.8555 (mtm) outliers start: 62 outliers final: 55 residues processed: 382 average time/residue: 0.3249 time to fit residues: 190.5741 Evaluate side-chains 394 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 338 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 604 CYS Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 647 GLU Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 40.0000 chunk 171 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 GLN I 6 GLN ** L 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.163870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129584 restraints weight = 28834.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129127 restraints weight = 24693.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130353 restraints weight = 28807.947| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 20467 Z= 0.272 Angle : 0.766 59.185 27840 Z= 0.426 Chirality : 0.045 0.341 3289 Planarity : 0.004 0.047 3480 Dihedral : 6.540 54.344 3794 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.62 % Favored : 95.05 % Rotamer: Outliers : 2.65 % Allowed : 19.92 % Favored : 77.44 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % 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: -0.70 (0.16), residues: 2466 helix: -0.38 (0.26), residues: 393 sheet: 0.44 (0.21), residues: 621 loop : -0.89 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 614 HIS 0.004 0.001 HIS C 35 PHE 0.009 0.001 PHE F 317 TYR 0.046 0.002 TYR F 361 ARG 0.005 0.000 ARG B 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4421.25 seconds wall clock time: 81 minutes 44.11 seconds (4904.11 seconds total)