Starting phenix.real_space_refine on Thu Feb 15 19:40:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de6_27385/02_2024/8de6_27385.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de6_27385/02_2024/8de6_27385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de6_27385/02_2024/8de6_27385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de6_27385/02_2024/8de6_27385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de6_27385/02_2024/8de6_27385.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de6_27385/02_2024/8de6_27385.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.144 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 101 5.16 5 C 8256 2.51 5 N 2271 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13243 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "B" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "C" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "G" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3202 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' CA': 1, 'BMA': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.22, per 1000 atoms: 0.55 Number of scatterers: 13243 At special positions: 0 Unit cell: (149.8, 119, 105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 101 16.00 O 2612 8.00 N 2271 7.00 C 8256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 114 " distance=2.02 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 107 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 67 " distance=2.05 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 104 " distance=2.05 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 113 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 460 " distance=2.03 Simple disulfide: pdb=" SG CYS A 447 " - pdb=" SG CYS A 462 " distance=2.02 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.00 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 107 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 57 " distance=2.04 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 91 " distance=2.05 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 113 " distance=2.05 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 160 " distance=2.02 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 460 " distance=2.04 Simple disulfide: pdb=" SG CYS C 447 " - pdb=" SG CYS C 462 " distance=2.01 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 57 " distance=2.04 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 67 " distance=2.04 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 73 " distance=2.02 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 86 " - pdb=" SG CYS G 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 113 " distance=2.04 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 160 " distance=2.03 Simple disulfide: pdb=" SG CYS G 444 " - pdb=" SG CYS G 460 " distance=2.02 Simple disulfide: pdb=" SG CYS G 447 " - pdb=" SG CYS G 462 " distance=2.02 Simple disulfide: pdb=" SG CYS G 464 " - pdb=" SG CYS G 473 " 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 Atom "HETATM13167 O5 BMA A 603 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Links applied NAG-THR " NAG A 601 " - " THR A 452 " " NAG C 601 " - " THR C 452 " " NAG G 601 " - " THR G 452 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.3 seconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 28 sheets defined 18.2% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.586A pdb=" N VAL E 50 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR E 51 " --> pdb=" O LEU E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.693A pdb=" N ASP E 108 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR E 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 109' Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.834A pdb=" N ASP A 112 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS A 113 " --> pdb=" O GLU A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 279 through 291 Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.614A pdb=" N GLU A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 removed outlier: 4.450A pdb=" N PHE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 411 through 414 removed outlier: 3.523A pdb=" N VAL A 414 " --> pdb=" O TYR A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 414' Processing helix chain 'A' and resid 420 through 438 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.596A pdb=" N LYS A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.899A pdb=" N VAL B 50 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 removed outlier: 3.695A pdb=" N LYS B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'I' and resid 98 through 102 removed outlier: 3.721A pdb=" N VAL I 102 " --> pdb=" O GLN I 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 109 through 113 removed outlier: 4.045A pdb=" N ASP C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS C 113 " --> pdb=" O GLU C 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 113' Processing helix chain 'C' and resid 129 through 134 removed outlier: 4.086A pdb=" N THR C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 369 through 381 removed outlier: 3.516A pdb=" N LEU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 396 removed outlier: 4.438A pdb=" N PHE C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 420 through 438 Processing helix chain 'C' and resid 440 through 444 removed outlier: 3.546A pdb=" N LYS C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 Processing helix chain 'G' and resid 109 through 113 removed outlier: 4.091A pdb=" N ASP G 112 " --> pdb=" O ASP G 109 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS G 113 " --> pdb=" O GLU G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'G' and resid 130 through 134 removed outlier: 3.949A pdb=" N THR G 134 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'G' and resid 279 through 291 Processing helix chain 'G' and resid 369 through 381 removed outlier: 3.834A pdb=" N ARG G 380 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY G 381 " --> pdb=" O LYS G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 396 removed outlier: 4.500A pdb=" N PHE G 389 " --> pdb=" O ASP G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 399 No H-bonds generated for 'chain 'G' and resid 397 through 399' Processing helix chain 'G' and resid 411 through 414 Processing helix chain 'G' and resid 420 through 438 Processing helix chain 'G' and resid 440 through 444 Processing sheet with id=AA1, first strand: chain 'E' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.809A pdb=" N VAL E 31 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 53 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N MET E 69 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP E 55 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.415A pdb=" N LEU F 30 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE F 67 " --> pdb=" O TRP F 54 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN F 56 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU F 65 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS F 58 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU F 63 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 38 through 43 removed outlier: 3.705A pdb=" N ASP F 89 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.909A pdb=" N ARG A 23 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 39 through 43 Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 128 removed outlier: 6.689A pdb=" N GLU A 127 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 170 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AB1, first strand: chain 'A' and resid 178 through 199 removed outlier: 6.002A pdb=" N VAL A 255 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 181 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG A 253 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR A 183 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU A 251 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N THR A 185 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE A 249 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N GLY A 187 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLY A 247 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS A 189 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N VAL A 245 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N PHE A 191 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N LEU A 243 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR A 193 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N MET A 241 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N HIS A 195 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLU A 239 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N GLU A 197 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LYS A 237 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 239 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 308 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 247 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 300 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 253 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY A 298 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 315 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 350 " --> pdb=" O ARG A 317 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 349 through 364 current: chain 'C' and resid 234 through 256 removed outlier: 3.882A pdb=" N LYS C 237 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 247 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 304 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 300 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG C 253 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY C 298 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 362 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 315 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 352 " --> pdb=" O MET C 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 351 through 364 current: chain 'G' and resid 237 through 256 removed outlier: 3.788A pdb=" N TYR G 308 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 247 " --> pdb=" O TYR G 304 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 300 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG G 253 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY G 298 " --> pdb=" O ARG G 253 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 303 " --> pdb=" O ARG G 364 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET G 315 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 352 " --> pdb=" O MET G 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 455 Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 24 removed outlier: 3.649A pdb=" N GLN B 96 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.695A pdb=" N VAL B 31 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 110 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 53 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET B 69 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP B 55 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.271A pdb=" N LEU I 30 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 38 through 43 removed outlier: 3.656A pdb=" N ASP I 89 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 72 through 73 removed outlier: 3.752A pdb=" N THR I 62 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS I 58 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS I 64 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP I 54 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU I 52 " --> pdb=" O TYR I 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.898A pdb=" N ARG C 23 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 39 through 43 removed outlier: 3.554A pdb=" N ARG C 42 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.665A pdb=" N GLY C 50 " --> pdb=" O CYS C 460 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N CYS C 462 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.813A pdb=" N GLU C 127 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 170 " --> pdb=" O ASP C 165 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AC5, first strand: chain 'G' and resid 23 through 24 removed outlier: 6.862A pdb=" N ARG G 23 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 39 through 43 Processing sheet with id=AC7, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'G' and resid 127 through 128 removed outlier: 6.618A pdb=" N GLU G 127 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR G 170 " --> pdb=" O ASP G 165 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 138 through 139 Processing sheet with id=AD1, first strand: chain 'G' and resid 452 through 455 372 hydrogen bonds defined for protein. 984 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: 3.33 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3630 1.33 - 1.46: 3616 1.46 - 1.59: 6121 1.59 - 1.72: 0 1.72 - 1.85: 134 Bond restraints: 13501 Sorted by residual: bond pdb=" C2 BMA C 602 " pdb=" O2 BMA C 602 " ideal model delta sigma weight residual 1.402 1.461 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C1 BMA G 603 " pdb=" C2 BMA G 603 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C ALA G 399 " pdb=" N PRO G 400 " ideal model delta sigma weight residual 1.328 1.298 0.030 1.25e-02 6.40e+03 5.61e+00 bond pdb=" C2 BMA C 602 " pdb=" C3 BMA C 602 " ideal model delta sigma weight residual 1.544 1.501 0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" CA ASP B 91 " pdb=" CB ASP B 91 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.27e-02 6.20e+03 4.66e+00 ... (remaining 13496 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.60: 232 105.60 - 112.89: 6973 112.89 - 120.17: 5080 120.17 - 127.46: 5821 127.46 - 134.75: 119 Bond angle restraints: 18225 Sorted by residual: angle pdb=" C ARG C 122 " pdb=" N ASP C 123 " pdb=" CA ASP C 123 " ideal model delta sigma weight residual 121.54 127.22 -5.68 1.91e+00 2.74e-01 8.85e+00 angle pdb=" N THR I 26 " pdb=" CA THR I 26 " pdb=" C THR I 26 " ideal model delta sigma weight residual 110.97 114.14 -3.17 1.09e+00 8.42e-01 8.48e+00 angle pdb=" N LEU G 407 " pdb=" CA LEU G 407 " pdb=" C LEU G 407 " ideal model delta sigma weight residual 110.28 114.47 -4.19 1.48e+00 4.57e-01 8.01e+00 angle pdb=" C4 BMA A 603 " pdb=" C5 BMA A 603 " pdb=" O5 BMA A 603 " ideal model delta sigma weight residual 113.24 105.35 7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C1 BMA C 602 " pdb=" O5 BMA C 602 " pdb=" C5 BMA C 602 " ideal model delta sigma weight residual 118.82 111.11 7.71 3.00e+00 1.11e-01 6.60e+00 ... (remaining 18220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 7966 22.75 - 45.51: 271 45.51 - 68.26: 31 68.26 - 91.01: 37 91.01 - 113.76: 24 Dihedral angle restraints: 8329 sinusoidal: 3547 harmonic: 4782 Sorted by residual: dihedral pdb=" O4 BMA A 602 " pdb=" C4 BMA A 602 " pdb=" C5 BMA A 602 " pdb=" O5 BMA A 602 " ideal model delta sinusoidal sigma weight residual 288.71 174.95 113.76 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O4 BMA A 603 " pdb=" C4 BMA A 603 " pdb=" C5 BMA A 603 " pdb=" O5 BMA A 603 " ideal model delta sinusoidal sigma weight residual 288.71 175.65 113.06 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" O4 BMA G 603 " pdb=" C4 BMA G 603 " pdb=" C5 BMA G 603 " pdb=" O5 BMA G 603 " ideal model delta sinusoidal sigma weight residual 288.71 177.12 111.59 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 8326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1498 0.067 - 0.135: 420 0.135 - 0.202: 55 0.202 - 0.270: 1 0.270 - 0.337: 6 Chirality restraints: 1980 Sorted by residual: chirality pdb=" C5 BMA C 602 " pdb=" C4 BMA C 602 " pdb=" C6 BMA C 602 " pdb=" O5 BMA C 602 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C2 BMA C 603 " pdb=" C1 BMA C 603 " pdb=" C3 BMA C 603 " pdb=" O2 BMA C 603 " both_signs ideal model delta sigma weight residual False 2.47 2.80 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 603 " pdb=" C4 BMA C 603 " pdb=" C6 BMA C 603 " pdb=" O5 BMA C 603 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1977 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 58 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO F 59 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 59 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 59 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 260 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C ASP G 260 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP G 260 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL G 261 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 54 " -0.001 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP F 54 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP F 54 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP F 54 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 54 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP F 54 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP F 54 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 54 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 54 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 54 " 0.019 2.00e-02 2.50e+03 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 556 2.72 - 3.26: 12048 3.26 - 3.81: 18695 3.81 - 4.35: 23607 4.35 - 4.90: 42554 Nonbonded interactions: 97460 Sorted by model distance: nonbonded pdb=" OD2 ASP G 270 " pdb=" OH TYR G 290 " model vdw 2.169 2.440 nonbonded pdb=" OD2 ASP A 270 " pdb=" OH TYR A 290 " model vdw 2.198 2.440 nonbonded pdb=" OD2 ASP G 109 " pdb="CA CA G 604 " model vdw 2.203 2.510 nonbonded pdb=" OG1 THR A 452 " pdb=" N2 NAG A 601 " model vdw 2.256 2.496 nonbonded pdb=" OG1 THR G 452 " pdb=" N2 NAG G 601 " model vdw 2.268 2.496 ... (remaining 97455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 4.320 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 34.530 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.010 0.071 13501 Z= 0.669 Angle : 0.928 7.885 18225 Z= 0.521 Chirality : 0.061 0.337 1980 Planarity : 0.007 0.058 2359 Dihedral : 14.683 113.764 5167 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.53 % Allowed : 6.76 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1633 helix: -0.06 (0.30), residues: 219 sheet: -0.28 (0.22), residues: 512 loop : -0.83 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.008 TRP C 30 HIS 0.018 0.005 HIS G 244 PHE 0.024 0.006 PHE A 389 TYR 0.026 0.006 TYR G 290 ARG 0.021 0.004 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 312 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 GLN cc_start: 0.8830 (pt0) cc_final: 0.8275 (pt0) REVERT: E 96 GLN cc_start: 0.9015 (mt0) cc_final: 0.8814 (mt0) REVERT: E 100 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7666 (mmmm) REVERT: F 43 ARG cc_start: 0.7276 (ttp80) cc_final: 0.7051 (mtm110) REVERT: A 56 ARG cc_start: 0.7733 (ptp90) cc_final: 0.7455 (ptp-110) REVERT: A 77 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7662 (pm20) REVERT: A 234 TYR cc_start: 0.7316 (t80) cc_final: 0.7076 (t80) REVERT: A 241 MET cc_start: 0.8640 (ttm) cc_final: 0.8380 (ttp) REVERT: A 250 HIS cc_start: 0.8653 (m-70) cc_final: 0.7784 (t70) REVERT: A 269 ASP cc_start: 0.8576 (m-30) cc_final: 0.8122 (m-30) REVERT: A 406 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8317 (ttmm) REVERT: A 433 GLU cc_start: 0.7711 (tt0) cc_final: 0.7130 (mt-10) REVERT: A 456 MET cc_start: 0.8051 (mmm) cc_final: 0.7791 (mmm) REVERT: B 62 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7156 (mmtm) REVERT: B 91 ASP cc_start: 0.7310 (t0) cc_final: 0.6843 (t70) REVERT: B 100 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6960 (mmtt) REVERT: B 108 ASP cc_start: 0.7820 (m-30) cc_final: 0.7560 (m-30) REVERT: I 23 MET cc_start: 0.8661 (mmm) cc_final: 0.8418 (mmm) REVERT: I 82 SER cc_start: 0.7802 (m) cc_final: 0.7526 (p) REVERT: I 96 ASN cc_start: 0.7923 (m110) cc_final: 0.7701 (m110) REVERT: I 123 LEU cc_start: 0.7649 (tp) cc_final: 0.7427 (tt) REVERT: C 23 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.8017 (ttp80) REVERT: C 101 ASP cc_start: 0.7324 (m-30) cc_final: 0.7080 (m-30) REVERT: C 107 PHE cc_start: 0.7059 (m-80) cc_final: 0.6851 (m-80) REVERT: C 171 TYR cc_start: 0.8195 (m-80) cc_final: 0.7969 (m-80) REVERT: C 182 ILE cc_start: 0.8512 (mt) cc_final: 0.8086 (mp) REVERT: C 185 THR cc_start: 0.8177 (m) cc_final: 0.7917 (p) REVERT: C 192 ARG cc_start: 0.6929 (ttm170) cc_final: 0.6351 (mmp80) REVERT: C 240 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7668 (mmtp) REVERT: C 251 LEU cc_start: 0.8401 (tp) cc_final: 0.8129 (tp) REVERT: C 272 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7869 (mtpp) REVERT: G 19 HIS cc_start: 0.6191 (p-80) cc_final: 0.5979 (p90) REVERT: G 45 SER cc_start: 0.7802 (t) cc_final: 0.7524 (p) REVERT: G 56 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6902 (ptm160) REVERT: G 79 ASP cc_start: 0.7531 (m-30) cc_final: 0.7263 (p0) REVERT: G 269 ASP cc_start: 0.8023 (m-30) cc_final: 0.7514 (m-30) REVERT: G 270 ASP cc_start: 0.7994 (m-30) cc_final: 0.7711 (m-30) REVERT: G 315 MET cc_start: 0.7638 (ttp) cc_final: 0.7357 (tmm) REVERT: G 379 LEU cc_start: 0.8084 (tp) cc_final: 0.7741 (tp) REVERT: G 406 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7949 (tmtt) REVERT: G 459 LYS cc_start: 0.7790 (tttm) cc_final: 0.7378 (tttt) outliers start: 37 outliers final: 20 residues processed: 339 average time/residue: 0.3026 time to fit residues: 139.7578 Evaluate side-chains 246 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 225 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 453 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 20 GLN E 96 GLN F 25 GLN A 32 GLN A 153 ASN A 177 ASN A 199 GLN B 20 GLN C 39 GLN C 177 ASN C 293 HIS C 354 ASN C 448 GLN C 449 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN G 177 ASN G 449 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13501 Z= 0.159 Angle : 0.512 5.938 18225 Z= 0.265 Chirality : 0.042 0.159 1980 Planarity : 0.004 0.051 2359 Dihedral : 11.525 71.159 2038 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.94 % Allowed : 10.52 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1633 helix: 0.81 (0.33), residues: 225 sheet: -0.18 (0.22), residues: 572 loop : -0.74 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 66 HIS 0.002 0.001 HIS C 244 PHE 0.009 0.001 PHE I 81 TYR 0.012 0.001 TYR A 294 ARG 0.004 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 231 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 GLN cc_start: 0.8867 (mt0) cc_final: 0.8600 (mt0) REVERT: E 100 LYS cc_start: 0.7839 (mmtm) cc_final: 0.7565 (mmmm) REVERT: F 26 THR cc_start: 0.8532 (p) cc_final: 0.8073 (p) REVERT: A 56 ARG cc_start: 0.7638 (ptp90) cc_final: 0.7279 (ptp-110) REVERT: A 77 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7661 (pm20) REVERT: A 192 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8016 (ttm110) REVERT: A 234 TYR cc_start: 0.7260 (t80) cc_final: 0.6957 (t80) REVERT: A 250 HIS cc_start: 0.8689 (m-70) cc_final: 0.7814 (t70) REVERT: A 369 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8111 (tttm) REVERT: A 406 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8243 (ttmm) REVERT: A 433 GLU cc_start: 0.7701 (tt0) cc_final: 0.7126 (mt-10) REVERT: A 456 MET cc_start: 0.8032 (mmm) cc_final: 0.7715 (mmm) REVERT: B 22 GLN cc_start: 0.7951 (mt0) cc_final: 0.7745 (mt0) REVERT: B 82 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8491 (pp) REVERT: B 91 ASP cc_start: 0.6963 (t0) cc_final: 0.6376 (t70) REVERT: B 100 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7102 (mmmt) REVERT: B 132 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7672 (tp-100) REVERT: I 23 MET cc_start: 0.8740 (mmm) cc_final: 0.8190 (mmm) REVERT: C 24 MET cc_start: 0.8968 (mtp) cc_final: 0.8751 (mmm) REVERT: C 101 ASP cc_start: 0.7389 (m-30) cc_final: 0.7163 (m-30) REVERT: C 182 ILE cc_start: 0.8778 (mt) cc_final: 0.8387 (tt) REVERT: C 188 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7603 (mt-10) REVERT: C 192 ARG cc_start: 0.7098 (ttm170) cc_final: 0.6400 (mmp80) REVERT: C 240 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7896 (mmtp) REVERT: C 243 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8085 (mm) REVERT: C 272 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7801 (tttm) REVERT: G 19 HIS cc_start: 0.6253 (p-80) cc_final: 0.6013 (p90) REVERT: G 56 ARG cc_start: 0.7394 (ptp90) cc_final: 0.7093 (ptm160) REVERT: G 79 ASP cc_start: 0.7715 (m-30) cc_final: 0.7483 (p0) REVERT: G 269 ASP cc_start: 0.8016 (m-30) cc_final: 0.7589 (m-30) REVERT: G 282 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7738 (mm-30) REVERT: G 376 GLU cc_start: 0.7210 (tp30) cc_final: 0.6629 (tt0) REVERT: G 453 VAL cc_start: 0.7901 (t) cc_final: 0.7552 (p) REVERT: G 459 LYS cc_start: 0.7601 (tttm) cc_final: 0.7388 (tttt) outliers start: 43 outliers final: 23 residues processed: 264 average time/residue: 0.3076 time to fit residues: 110.8096 Evaluate side-chains 238 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 396 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN G 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13501 Z= 0.407 Angle : 0.632 7.356 18225 Z= 0.334 Chirality : 0.047 0.169 1980 Planarity : 0.005 0.053 2359 Dihedral : 8.756 59.930 2027 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.10 % Allowed : 12.43 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1633 helix: 0.41 (0.33), residues: 225 sheet: -0.24 (0.22), residues: 534 loop : -1.14 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 27 HIS 0.005 0.001 HIS C 293 PHE 0.018 0.002 PHE C 191 TYR 0.023 0.002 TYR B 113 ARG 0.008 0.001 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 208 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7629 (mmmm) REVERT: A 149 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9206 (p) REVERT: A 192 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8025 (ttm110) REVERT: A 234 TYR cc_start: 0.7984 (t80) cc_final: 0.7633 (t80) REVERT: A 241 MET cc_start: 0.8694 (ttp) cc_final: 0.8312 (ttp) REVERT: A 250 HIS cc_start: 0.8725 (m-70) cc_final: 0.7799 (t70) REVERT: A 260 ASP cc_start: 0.8709 (t0) cc_final: 0.8474 (t0) REVERT: A 369 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8095 (tttm) REVERT: A 406 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8114 (ttmm) REVERT: A 433 GLU cc_start: 0.7823 (tt0) cc_final: 0.7248 (mt-10) REVERT: A 456 MET cc_start: 0.8230 (mmm) cc_final: 0.7995 (mmm) REVERT: B 82 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8529 (pp) REVERT: B 91 ASP cc_start: 0.7029 (t0) cc_final: 0.6349 (t70) REVERT: B 100 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6939 (mmmt) REVERT: B 132 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7549 (tp-100) REVERT: I 23 MET cc_start: 0.8964 (mmm) cc_final: 0.8369 (mmm) REVERT: C 101 ASP cc_start: 0.7226 (m-30) cc_final: 0.6996 (m-30) REVERT: C 164 ARG cc_start: 0.8330 (ttt90) cc_final: 0.8100 (ttt90) REVERT: C 169 LEU cc_start: 0.8719 (mp) cc_final: 0.8389 (tp) REVERT: C 192 ARG cc_start: 0.7239 (ttm170) cc_final: 0.6781 (mmt-90) REVERT: C 240 LYS cc_start: 0.8456 (mtmt) cc_final: 0.7927 (mmtp) REVERT: C 243 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8139 (mm) REVERT: C 272 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7922 (tttm) REVERT: G 56 ARG cc_start: 0.7466 (ptp90) cc_final: 0.7112 (ptm160) REVERT: G 79 ASP cc_start: 0.7812 (m-30) cc_final: 0.7375 (p0) REVERT: G 376 GLU cc_start: 0.7338 (tp30) cc_final: 0.6915 (tt0) REVERT: G 406 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7779 (tmtt) REVERT: G 453 VAL cc_start: 0.8030 (t) cc_final: 0.7744 (p) REVERT: G 459 LYS cc_start: 0.7797 (tttm) cc_final: 0.7481 (tttt) REVERT: G 477 LYS cc_start: 0.6340 (OUTLIER) cc_final: 0.5621 (tppt) outliers start: 60 outliers final: 36 residues processed: 256 average time/residue: 0.3021 time to fit residues: 105.9599 Evaluate side-chains 235 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 250 HIS Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13501 Z= 0.155 Angle : 0.483 8.802 18225 Z= 0.255 Chirality : 0.041 0.150 1980 Planarity : 0.003 0.049 2359 Dihedral : 6.964 59.749 2025 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.55 % Allowed : 13.66 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1633 helix: 0.82 (0.34), residues: 225 sheet: -0.14 (0.22), residues: 554 loop : -1.02 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 66 HIS 0.002 0.001 HIS I 46 PHE 0.013 0.001 PHE G 466 TYR 0.015 0.001 TYR B 113 ARG 0.006 0.000 ARG I 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7430 (mmmm) REVERT: A 77 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7716 (pm20) REVERT: A 149 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.9253 (p) REVERT: A 192 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8043 (ttm110) REVERT: A 234 TYR cc_start: 0.7828 (t80) cc_final: 0.7440 (t80) REVERT: A 250 HIS cc_start: 0.8685 (m-70) cc_final: 0.7790 (t70) REVERT: A 369 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8126 (tttm) REVERT: A 406 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8103 (ttmm) REVERT: A 433 GLU cc_start: 0.7713 (tt0) cc_final: 0.7116 (mt-10) REVERT: B 22 GLN cc_start: 0.8186 (mt0) cc_final: 0.7962 (mt0) REVERT: B 62 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7417 (mmtm) REVERT: B 82 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8477 (pp) REVERT: B 91 ASP cc_start: 0.7260 (t0) cc_final: 0.6675 (t70) REVERT: B 100 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6958 (mmmt) REVERT: B 132 GLN cc_start: 0.7867 (tp-100) cc_final: 0.7490 (tp-100) REVERT: I 23 MET cc_start: 0.8849 (mmm) cc_final: 0.8374 (mmm) REVERT: C 101 ASP cc_start: 0.7330 (m-30) cc_final: 0.7096 (m-30) REVERT: C 124 ARG cc_start: 0.6903 (mmp-170) cc_final: 0.6634 (mmp-170) REVERT: C 169 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8444 (tp) REVERT: C 182 ILE cc_start: 0.8796 (mt) cc_final: 0.8324 (tt) REVERT: C 188 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7294 (tt0) REVERT: C 192 ARG cc_start: 0.7092 (ttm170) cc_final: 0.6472 (mmp80) REVERT: C 272 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7911 (tttm) REVERT: G 56 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7129 (ptm160) REVERT: G 79 ASP cc_start: 0.7835 (m-30) cc_final: 0.7353 (p0) REVERT: G 376 GLU cc_start: 0.7283 (tp30) cc_final: 0.6886 (tt0) REVERT: G 453 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7759 (p) REVERT: G 459 LYS cc_start: 0.7660 (tttm) cc_final: 0.7353 (tttt) outliers start: 52 outliers final: 31 residues processed: 237 average time/residue: 0.2942 time to fit residues: 96.5570 Evaluate side-chains 227 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 405 GLN Chi-restraints excluded: chain G residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.0040 chunk 65 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 293 HIS C 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13501 Z= 0.133 Angle : 0.457 9.785 18225 Z= 0.240 Chirality : 0.040 0.146 1980 Planarity : 0.003 0.048 2359 Dihedral : 5.955 59.012 2023 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.35 % Allowed : 14.21 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1633 helix: 0.98 (0.34), residues: 228 sheet: -0.04 (0.22), residues: 554 loop : -0.97 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 66 HIS 0.004 0.001 HIS A 445 PHE 0.015 0.001 PHE G 466 TYR 0.012 0.001 TYR B 113 ARG 0.007 0.000 ARG I 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7285 (mmmm) REVERT: A 77 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7723 (pm20) REVERT: A 149 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9232 (p) REVERT: A 192 ARG cc_start: 0.8354 (ttm110) cc_final: 0.8117 (ttm-80) REVERT: A 199 GLN cc_start: 0.7900 (mt0) cc_final: 0.7509 (mt0) REVERT: A 234 TYR cc_start: 0.7788 (t80) cc_final: 0.7371 (t80) REVERT: A 250 HIS cc_start: 0.8649 (m-70) cc_final: 0.8409 (m90) REVERT: A 369 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8110 (tttp) REVERT: A 406 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8103 (ttmt) REVERT: A 433 GLU cc_start: 0.7685 (tt0) cc_final: 0.7088 (mt-10) REVERT: B 22 GLN cc_start: 0.8248 (mt0) cc_final: 0.8009 (mt0) REVERT: B 62 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7315 (mmtm) REVERT: B 82 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8470 (pp) REVERT: B 91 ASP cc_start: 0.7112 (t0) cc_final: 0.6501 (t70) REVERT: B 100 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6988 (mmmt) REVERT: B 132 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7420 (tp-100) REVERT: I 23 MET cc_start: 0.8834 (mmm) cc_final: 0.8377 (mmm) REVERT: C 101 ASP cc_start: 0.7313 (m-30) cc_final: 0.7078 (m-30) REVERT: C 162 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7722 (ptm160) REVERT: C 182 ILE cc_start: 0.8795 (mt) cc_final: 0.8351 (tt) REVERT: C 188 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7222 (tt0) REVERT: C 192 ARG cc_start: 0.7072 (ttm170) cc_final: 0.6480 (mmp80) REVERT: C 272 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7898 (tttm) REVERT: G 56 ARG cc_start: 0.7551 (ptp90) cc_final: 0.7231 (ptm160) REVERT: G 79 ASP cc_start: 0.7852 (m-30) cc_final: 0.7389 (p0) REVERT: G 376 GLU cc_start: 0.7223 (tp30) cc_final: 0.6882 (tt0) REVERT: G 453 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7758 (p) REVERT: G 459 LYS cc_start: 0.7547 (tttm) cc_final: 0.7263 (tttt) REVERT: G 477 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5245 (tppt) outliers start: 49 outliers final: 36 residues processed: 239 average time/residue: 0.2975 time to fit residues: 98.7633 Evaluate side-chains 236 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 405 GLN Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 0.0060 chunk 83 optimal weight: 2.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN G 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13501 Z= 0.415 Angle : 0.622 10.249 18225 Z= 0.329 Chirality : 0.045 0.181 1980 Planarity : 0.005 0.053 2359 Dihedral : 6.464 59.552 2023 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.96 % Allowed : 14.75 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1633 helix: 0.44 (0.34), residues: 225 sheet: -0.31 (0.22), residues: 546 loop : -1.26 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 27 HIS 0.005 0.001 HIS A 293 PHE 0.017 0.002 PHE C 191 TYR 0.024 0.002 TYR B 113 ARG 0.006 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 196 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.7325 (m90) REVERT: A 77 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7733 (pm20) REVERT: A 149 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9259 (p) REVERT: A 241 MET cc_start: 0.8606 (ttm) cc_final: 0.8361 (ttp) REVERT: A 250 HIS cc_start: 0.8709 (m-70) cc_final: 0.8485 (m90) REVERT: A 353 GLU cc_start: 0.7737 (mp0) cc_final: 0.6932 (mp0) REVERT: A 406 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8136 (ttmm) REVERT: B 62 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7369 (mmtm) REVERT: B 82 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8559 (pp) REVERT: B 91 ASP cc_start: 0.7278 (t0) cc_final: 0.6643 (t70) REVERT: B 100 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6905 (mmmt) REVERT: B 132 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7675 (tp-100) REVERT: C 101 ASP cc_start: 0.7142 (m-30) cc_final: 0.6899 (m-30) REVERT: C 124 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6628 (mmp-170) REVERT: C 162 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7797 (ptm160) REVERT: C 192 ARG cc_start: 0.7280 (ttm170) cc_final: 0.6809 (mmt-90) REVERT: C 272 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7937 (tttm) REVERT: G 56 ARG cc_start: 0.7517 (ptp90) cc_final: 0.7132 (ptm160) REVERT: G 79 ASP cc_start: 0.7953 (m-30) cc_final: 0.7446 (p0) REVERT: G 384 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6571 (tt) REVERT: G 459 LYS cc_start: 0.7647 (tttm) cc_final: 0.7343 (tttt) REVERT: G 477 LYS cc_start: 0.6355 (OUTLIER) cc_final: 0.5615 (tppt) outliers start: 58 outliers final: 44 residues processed: 239 average time/residue: 0.2912 time to fit residues: 96.2225 Evaluate side-chains 245 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 193 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 250 HIS Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 98 optimal weight: 0.0970 chunk 96 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13501 Z= 0.128 Angle : 0.476 11.177 18225 Z= 0.252 Chirality : 0.040 0.148 1980 Planarity : 0.003 0.049 2359 Dihedral : 5.748 58.468 2023 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.07 % Allowed : 16.73 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1633 helix: 0.86 (0.34), residues: 225 sheet: -0.19 (0.22), residues: 555 loop : -1.09 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 27 HIS 0.021 0.001 HIS F 46 PHE 0.010 0.001 PHE C 267 TYR 0.017 0.001 TYR A 234 ARG 0.007 0.000 ARG I 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7766 (mmmm) cc_final: 0.7466 (mmmm) REVERT: A 77 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7690 (pm20) REVERT: A 199 GLN cc_start: 0.7859 (mt0) cc_final: 0.7521 (mt0) REVERT: A 353 GLU cc_start: 0.7736 (mp0) cc_final: 0.6935 (mp0) REVERT: A 406 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8095 (ttmm) REVERT: A 433 GLU cc_start: 0.7699 (tt0) cc_final: 0.7101 (mt-10) REVERT: B 62 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7392 (mmtm) REVERT: B 82 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8522 (pp) REVERT: B 91 ASP cc_start: 0.7095 (t0) cc_final: 0.6459 (t70) REVERT: B 100 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6857 (mmmt) REVERT: B 132 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7508 (tp-100) REVERT: C 101 ASP cc_start: 0.7274 (m-30) cc_final: 0.7008 (m-30) REVERT: C 124 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6772 (mmp80) REVERT: C 182 ILE cc_start: 0.8795 (mt) cc_final: 0.8337 (tt) REVERT: C 192 ARG cc_start: 0.7143 (ttm170) cc_final: 0.6534 (mmp80) REVERT: C 272 LYS cc_start: 0.8435 (ttmt) cc_final: 0.7926 (tttm) REVERT: G 56 ARG cc_start: 0.7572 (ptp90) cc_final: 0.7233 (ptm160) REVERT: G 79 ASP cc_start: 0.7933 (m-30) cc_final: 0.7513 (p0) REVERT: G 453 VAL cc_start: 0.8083 (t) cc_final: 0.7865 (p) REVERT: G 459 LYS cc_start: 0.7476 (tttm) cc_final: 0.7187 (tttt) outliers start: 45 outliers final: 33 residues processed: 229 average time/residue: 0.2891 time to fit residues: 91.9631 Evaluate side-chains 224 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 124 optimal weight: 0.0670 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS I 50 ASN C 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13501 Z= 0.215 Angle : 0.507 11.910 18225 Z= 0.268 Chirality : 0.041 0.146 1980 Planarity : 0.004 0.050 2359 Dihedral : 5.737 58.557 2023 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.42 % Allowed : 16.60 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1633 helix: 0.78 (0.34), residues: 225 sheet: -0.22 (0.22), residues: 555 loop : -1.13 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 27 HIS 0.004 0.001 HIS F 46 PHE 0.010 0.001 PHE A 155 TYR 0.016 0.001 TYR B 113 ARG 0.009 0.000 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7692 (pm20) REVERT: A 199 GLN cc_start: 0.7788 (mt0) cc_final: 0.7348 (mt0) REVERT: A 353 GLU cc_start: 0.7726 (mp0) cc_final: 0.6934 (mp0) REVERT: A 406 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8106 (ttmm) REVERT: A 433 GLU cc_start: 0.7705 (tt0) cc_final: 0.7099 (mt-10) REVERT: B 62 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7365 (mmtm) REVERT: B 82 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8516 (pp) REVERT: B 91 ASP cc_start: 0.7096 (t0) cc_final: 0.6482 (t70) REVERT: B 100 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6867 (mmmt) REVERT: B 132 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7617 (tp-100) REVERT: C 101 ASP cc_start: 0.7121 (m-30) cc_final: 0.6863 (m-30) REVERT: C 162 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7918 (ptm-80) REVERT: C 182 ILE cc_start: 0.8779 (mt) cc_final: 0.8296 (tt) REVERT: C 192 ARG cc_start: 0.7251 (ttm170) cc_final: 0.6771 (mmp80) REVERT: C 272 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7944 (tttm) REVERT: G 56 ARG cc_start: 0.7596 (ptp90) cc_final: 0.7238 (ptm160) REVERT: G 79 ASP cc_start: 0.7976 (m-30) cc_final: 0.7607 (p0) REVERT: G 198 GLU cc_start: 0.6738 (mp0) cc_final: 0.6349 (tt0) REVERT: G 406 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7650 (tmtt) REVERT: G 453 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7942 (p) REVERT: G 459 LYS cc_start: 0.7501 (tttm) cc_final: 0.7213 (tttt) REVERT: G 477 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5850 (tppt) outliers start: 50 outliers final: 38 residues processed: 230 average time/residue: 0.2957 time to fit residues: 94.9325 Evaluate side-chains 232 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 406 LYS Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13501 Z= 0.374 Angle : 0.600 12.539 18225 Z= 0.318 Chirality : 0.044 0.150 1980 Planarity : 0.004 0.052 2359 Dihedral : 6.273 59.288 2023 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.62 % Allowed : 16.94 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1633 helix: 0.39 (0.34), residues: 225 sheet: -0.39 (0.22), residues: 546 loop : -1.36 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 66 HIS 0.005 0.001 HIS I 46 PHE 0.014 0.002 PHE C 254 TYR 0.021 0.002 TYR B 113 ARG 0.007 0.001 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 198 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7260 (m90) REVERT: A 77 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7734 (pm20) REVERT: A 353 GLU cc_start: 0.7716 (mp0) cc_final: 0.7119 (mp0) REVERT: A 406 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8082 (ttmm) REVERT: B 62 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7363 (mmtm) REVERT: B 82 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8584 (pp) REVERT: B 91 ASP cc_start: 0.7153 (t0) cc_final: 0.6455 (t70) REVERT: B 100 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6827 (mmmt) REVERT: B 105 GLN cc_start: 0.8220 (mt0) cc_final: 0.7759 (mp-120) REVERT: B 132 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7520 (tp-100) REVERT: C 101 ASP cc_start: 0.7116 (m-30) cc_final: 0.6867 (m-30) REVERT: C 162 ARG cc_start: 0.8180 (ptm160) cc_final: 0.7967 (ptm-80) REVERT: C 192 ARG cc_start: 0.7274 (ttm170) cc_final: 0.6839 (mmt-90) REVERT: C 272 LYS cc_start: 0.8507 (ttmt) cc_final: 0.7960 (tttm) REVERT: G 56 ARG cc_start: 0.7581 (ptp90) cc_final: 0.7145 (ptm160) REVERT: G 79 ASP cc_start: 0.8027 (m-30) cc_final: 0.7696 (p0) REVERT: G 406 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7759 (tmtt) REVERT: G 453 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7985 (p) REVERT: G 459 LYS cc_start: 0.7568 (tttm) cc_final: 0.7279 (tttt) REVERT: G 477 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.5645 (tppt) outliers start: 53 outliers final: 40 residues processed: 241 average time/residue: 0.2814 time to fit residues: 94.3280 Evaluate side-chains 240 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 194 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 46 HIS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 406 LYS Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13501 Z= 0.175 Angle : 0.510 12.908 18225 Z= 0.269 Chirality : 0.041 0.147 1980 Planarity : 0.003 0.050 2359 Dihedral : 5.867 57.584 2023 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.87 % Allowed : 17.62 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1633 helix: 0.68 (0.35), residues: 225 sheet: -0.33 (0.22), residues: 549 loop : -1.23 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 27 HIS 0.009 0.001 HIS F 46 PHE 0.012 0.001 PHE G 466 TYR 0.015 0.001 TYR B 113 ARG 0.007 0.000 ARG I 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 192 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7692 (pm20) REVERT: A 199 GLN cc_start: 0.7862 (mt0) cc_final: 0.7437 (mt0) REVERT: A 353 GLU cc_start: 0.7726 (mp0) cc_final: 0.6935 (mp0) REVERT: A 406 LYS cc_start: 0.8764 (ttpp) cc_final: 0.8077 (ttmm) REVERT: B 22 GLN cc_start: 0.8354 (mt0) cc_final: 0.8148 (mt0) REVERT: B 62 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7336 (mmtm) REVERT: B 91 ASP cc_start: 0.7035 (t0) cc_final: 0.6365 (t70) REVERT: B 100 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6849 (mmmt) REVERT: B 105 GLN cc_start: 0.8159 (mt0) cc_final: 0.7732 (mp-120) REVERT: B 132 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7515 (tp-100) REVERT: C 101 ASP cc_start: 0.7127 (m-30) cc_final: 0.6869 (m-30) REVERT: C 162 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7832 (ptm160) REVERT: C 192 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6712 (mmp80) REVERT: C 197 GLU cc_start: 0.8417 (pt0) cc_final: 0.8098 (mt-10) REVERT: C 272 LYS cc_start: 0.8457 (ttmt) cc_final: 0.7932 (tttm) REVERT: G 56 ARG cc_start: 0.7670 (ptp90) cc_final: 0.7257 (ptm160) REVERT: G 79 ASP cc_start: 0.8012 (m-30) cc_final: 0.7706 (p0) REVERT: G 198 GLU cc_start: 0.6822 (mp0) cc_final: 0.6432 (tt0) REVERT: G 406 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7681 (tmtt) REVERT: G 459 LYS cc_start: 0.7477 (tttm) cc_final: 0.7205 (tttt) REVERT: G 477 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5812 (tppt) outliers start: 42 outliers final: 36 residues processed: 225 average time/residue: 0.2937 time to fit residues: 91.4941 Evaluate side-chains 228 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 406 LYS Chi-restraints excluded: chain G residue 447 CYS Chi-restraints excluded: chain G residue 454 ILE Chi-restraints excluded: chain G residue 477 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.0000 chunk 130 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 HIS C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103980 restraints weight = 16486.259| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.50 r_work: 0.3079 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13501 Z= 0.244 Angle : 0.528 13.121 18225 Z= 0.279 Chirality : 0.042 0.145 1980 Planarity : 0.004 0.050 2359 Dihedral : 5.850 58.036 2023 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.14 % Allowed : 17.62 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1633 helix: 0.59 (0.35), residues: 225 sheet: -0.36 (0.22), residues: 549 loop : -1.26 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 27 HIS 0.005 0.001 HIS I 46 PHE 0.011 0.002 PHE A 155 TYR 0.017 0.002 TYR E 113 ARG 0.007 0.000 ARG I 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3084.14 seconds wall clock time: 56 minutes 31.07 seconds (3391.07 seconds total)