Starting phenix.real_space_refine on Fri Feb 16 08:37:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ur8_20857/02_2024/6ur8_20857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ur8_20857/02_2024/6ur8_20857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ur8_20857/02_2024/6ur8_20857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ur8_20857/02_2024/6ur8_20857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ur8_20857/02_2024/6ur8_20857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ur8_20857/02_2024/6ur8_20857_updated.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 9779 2.51 5 N 2357 2.21 5 O 2651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ASP 34": "OD1" <-> "OD2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 573": "OD1" <-> "OD2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 236": "OD1" <-> "OD2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 236": "OD1" <-> "OD2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 573": "OD1" <-> "OD2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 179": "OD1" <-> "OD2" Residue "E ASP 192": "OD1" <-> "OD2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 236": "OD1" <-> "OD2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2976 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 343} Chain breaks: 1 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "D" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2976 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 343} Chain breaks: 1 Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.12, per 1000 atoms: 0.55 Number of scatterers: 14880 At special positions: 0 Unit cell: (144.414, 95.9088, 120.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 2651 8.00 N 2357 7.00 C 9779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.7 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 18 sheets defined 33.9% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 248 through 268 removed outlier: 4.702A pdb=" N GLU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 318 through 328 Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 565 through 592 removed outlier: 3.514A pdb=" N MET A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.227A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 4.393A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 240 through 261 Processing helix chain 'B' and resid 271 through 297 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.543A pdb=" N VAL B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 314 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 315 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 334 through 364 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.227A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 4.393A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 240 through 261 Processing helix chain 'C' and resid 271 through 297 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.542A pdb=" N VAL C 312 " --> pdb=" O TRP C 309 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 314 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 315 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 316 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU C 318 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Proline residue: C 319 - end of helix Processing helix chain 'C' and resid 334 through 364 Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 248 through 268 removed outlier: 4.702A pdb=" N GLU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 305 Processing helix chain 'D' and resid 318 through 328 Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 566 through 592 removed outlier: 3.514A pdb=" N MET D 579 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.227A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix removed outlier: 4.392A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 271 through 298 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.543A pdb=" N VAL E 312 " --> pdb=" O TRP E 309 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE E 314 " --> pdb=" O LYS E 311 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 315 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU E 316 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU E 318 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Proline residue: E 319 - end of helix Processing helix chain 'E' and resid 334 through 364 Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.668A pdb=" N VAL A 36 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 166 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 38 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.875A pdb=" N ASP A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.707A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.484A pdb=" N VAL B 31 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 33 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR B 32 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU B 63 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN B 55 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 58 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= F, first strand: chain 'B' and resid 79 through 82 Processing sheet with id= G, first strand: chain 'B' and resid 141 through 148 removed outlier: 3.770A pdb=" N ALA B 182 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG B 206 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B 180 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.484A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 58 " --> pdb=" O PRO C 122 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= J, first strand: chain 'C' and resid 79 through 82 Processing sheet with id= K, first strand: chain 'C' and resid 141 through 148 removed outlier: 3.770A pdb=" N ALA C 182 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG C 206 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C 180 " --> pdb=" O ARG C 206 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.667A pdb=" N VAL D 36 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL D 166 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL D 38 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.874A pdb=" N ASP D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.707A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.483A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 58 " --> pdb=" O PRO E 122 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 44 through 46 Processing sheet with id= Q, first strand: chain 'E' and resid 79 through 82 Processing sheet with id= R, first strand: chain 'E' and resid 141 through 148 removed outlier: 3.770A pdb=" N ALA E 182 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2296 1.31 - 1.44: 4244 1.44 - 1.57: 8596 1.57 - 1.70: 6 1.70 - 1.82: 151 Bond restraints: 15293 Sorted by residual: bond pdb=" C05 QMR D 702 " pdb=" C06 QMR D 702 " ideal model delta sigma weight residual 1.536 1.224 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" C05 QMR A 702 " pdb=" C06 QMR A 702 " ideal model delta sigma weight residual 1.536 1.225 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C04 QMR A 702 " pdb=" C05 QMR A 702 " ideal model delta sigma weight residual 1.536 1.229 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C04 QMR D 702 " pdb=" C05 QMR D 702 " ideal model delta sigma weight residual 1.536 1.229 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C04 QMR D 702 " pdb=" C16 QMR D 702 " ideal model delta sigma weight residual 1.507 1.730 -0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 15288 not shown) Histogram of bond angle deviations from ideal: 97.53 - 106.51: 505 106.51 - 115.48: 9696 115.48 - 124.46: 10247 124.46 - 133.43: 376 133.43 - 142.41: 60 Bond angle restraints: 20884 Sorted by residual: angle pdb=" C ASP D 564 " pdb=" N TRP D 565 " pdb=" CA TRP D 565 " ideal model delta sigma weight residual 120.29 129.37 -9.08 1.42e+00 4.96e-01 4.09e+01 angle pdb=" CB ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CD1 ILE A 222 " ideal model delta sigma weight residual 113.80 122.87 -9.07 2.10e+00 2.27e-01 1.87e+01 angle pdb=" C04 QMR D 702 " pdb=" C05 QMR D 702 " pdb=" C06 QMR D 702 " ideal model delta sigma weight residual 100.12 113.02 -12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C04 QMR A 702 " pdb=" C05 QMR A 702 " pdb=" C06 QMR A 702 " ideal model delta sigma weight residual 100.12 113.02 -12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CA SER E 15 " pdb=" CB SER E 15 " pdb=" OG SER E 15 " ideal model delta sigma weight residual 111.10 119.66 -8.56 2.00e+00 2.50e-01 1.83e+01 ... (remaining 20879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.52: 8355 19.52 - 39.05: 731 39.05 - 58.57: 82 58.57 - 78.09: 21 78.09 - 97.62: 14 Dihedral angle restraints: 9203 sinusoidal: 3847 harmonic: 5356 Sorted by residual: dihedral pdb=" CA MET C 324 " pdb=" C MET C 324 " pdb=" N GLN C 325 " pdb=" CA GLN C 325 " ideal model delta harmonic sigma weight residual 180.00 139.02 40.98 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA MET B 324 " pdb=" C MET B 324 " pdb=" N GLN B 325 " pdb=" CA GLN B 325 " ideal model delta harmonic sigma weight residual 180.00 139.06 40.94 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" CA MET E 324 " pdb=" C MET E 324 " pdb=" N GLN E 325 " pdb=" CA GLN E 325 " ideal model delta harmonic sigma weight residual 180.00 139.07 40.93 0 5.00e+00 4.00e-02 6.70e+01 ... (remaining 9200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2389 0.108 - 0.216: 55 0.216 - 0.324: 11 0.324 - 0.433: 2 0.433 - 0.541: 4 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CB THR A 273 " pdb=" CA THR A 273 " pdb=" OG1 THR A 273 " pdb=" CG2 THR A 273 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CB THR D 273 " pdb=" CA THR D 273 " pdb=" OG1 THR D 273 " pdb=" CG2 THR D 273 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" C06 QMR D 702 " pdb=" C01 QMR D 702 " pdb=" C05 QMR D 702 " pdb=" C07 QMR D 702 " both_signs ideal model delta sigma weight residual False -3.02 -2.56 -0.47 2.00e-01 2.50e+01 5.43e+00 ... (remaining 2458 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 564 " -0.015 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP D 564 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP D 564 " -0.022 2.00e-02 2.50e+03 pdb=" N TRP D 565 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 589 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C VAL A 589 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 589 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 590 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 589 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C VAL D 589 " 0.053 2.00e-02 2.50e+03 pdb=" O VAL D 589 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY D 590 " -0.018 2.00e-02 2.50e+03 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 122 2.56 - 3.14: 12521 3.14 - 3.73: 21203 3.73 - 4.31: 28825 4.31 - 4.90: 49340 Nonbonded interactions: 112011 Sorted by model distance: nonbonded pdb=" ND2 ASN C 97 " pdb=" O MET C 101 " model vdw 1.970 2.520 nonbonded pdb=" ND2 ASN E 97 " pdb=" O MET E 101 " model vdw 1.970 2.520 nonbonded pdb=" ND2 ASN B 97 " pdb=" O MET B 101 " model vdw 1.971 2.520 nonbonded pdb=" O MET E 324 " pdb=" OH TYR E 340 " model vdw 2.074 2.440 nonbonded pdb=" O MET B 324 " pdb=" OH TYR B 340 " model vdw 2.075 2.440 ... (remaining 112006 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 'D' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 7.310 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 41.330 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 0.312 15293 Z= 0.619 Angle : 0.859 12.903 20884 Z= 0.443 Chirality : 0.056 0.541 2461 Planarity : 0.005 0.074 2529 Dihedral : 14.861 97.615 5684 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.16), residues: 1778 helix: -2.17 (0.16), residues: 621 sheet: -2.86 (0.21), residues: 444 loop : -3.73 (0.19), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 151 HIS 0.002 0.001 HIS B 297 PHE 0.010 0.001 PHE A 322 TYR 0.012 0.001 TYR C 340 ARG 0.003 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: A 148 ASN cc_start: 0.8642 (t0) cc_final: 0.8441 (t0) REVERT: A 178 TRP cc_start: 0.8613 (t-100) cc_final: 0.8336 (t-100) REVERT: A 572 ILE cc_start: 0.7655 (tt) cc_final: 0.7395 (mt) REVERT: B 159 ASP cc_start: 0.7915 (t0) cc_final: 0.7588 (p0) REVERT: C 132 ILE cc_start: 0.8510 (mm) cc_final: 0.8268 (mm) REVERT: D 157 THR cc_start: 0.8664 (p) cc_final: 0.8358 (t) REVERT: D 570 MET cc_start: 0.7134 (ttm) cc_final: 0.6934 (ttt) REVERT: E 77 MET cc_start: 0.6904 (mtp) cc_final: 0.6693 (ttm) outliers start: 1 outliers final: 1 residues processed: 354 average time/residue: 0.2848 time to fit residues: 143.3784 Evaluate side-chains 203 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 589 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.3980 chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 312 HIS B 142 GLN C 109 ASN C 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15293 Z= 0.203 Angle : 0.684 9.603 20884 Z= 0.335 Chirality : 0.045 0.180 2461 Planarity : 0.004 0.045 2529 Dihedral : 5.813 33.213 2198 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.43 % Allowed : 10.40 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.18), residues: 1778 helix: 0.06 (0.20), residues: 623 sheet: -2.04 (0.23), residues: 410 loop : -2.98 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 151 HIS 0.008 0.001 HIS C 297 PHE 0.014 0.001 PHE A 322 TYR 0.010 0.001 TYR C 340 ARG 0.003 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 1.773 Fit side-chains REVERT: A 231 ILE cc_start: 0.8922 (pt) cc_final: 0.8309 (mt) REVERT: A 572 ILE cc_start: 0.7747 (tt) cc_final: 0.7507 (mt) REVERT: B 159 ASP cc_start: 0.7910 (t0) cc_final: 0.7625 (p0) REVERT: B 354 VAL cc_start: 0.8459 (p) cc_final: 0.8223 (t) REVERT: C 106 PHE cc_start: 0.7408 (t80) cc_final: 0.7015 (t80) REVERT: C 257 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8132 (mp) outliers start: 24 outliers final: 13 residues processed: 289 average time/residue: 0.2521 time to fit residues: 109.2065 Evaluate side-chains 216 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 202 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 596 TRP Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 0.0020 chunk 109 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 0.0170 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 129 optimal weight: 0.0570 overall best weight: 0.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN D 68 HIS E 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15293 Z= 0.172 Angle : 0.622 9.761 20884 Z= 0.304 Chirality : 0.043 0.161 2461 Planarity : 0.004 0.034 2529 Dihedral : 4.519 26.040 2197 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.14 % Allowed : 13.61 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -1.56 (0.19), residues: 1778 helix: 0.97 (0.21), residues: 609 sheet: -1.40 (0.24), residues: 410 loop : -2.55 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 351 HIS 0.007 0.001 HIS C 297 PHE 0.023 0.001 PHE B 359 TYR 0.011 0.001 TYR C 340 ARG 0.002 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 1.573 Fit side-chains REVERT: A 90 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 231 ILE cc_start: 0.8870 (pt) cc_final: 0.8517 (mt) REVERT: B 70 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8014 (mtpt) REVERT: B 95 TYR cc_start: 0.6271 (OUTLIER) cc_final: 0.5113 (m-80) REVERT: B 306 MET cc_start: 0.8133 (ptt) cc_final: 0.7832 (ptm) REVERT: B 354 VAL cc_start: 0.8489 (p) cc_final: 0.8260 (t) REVERT: C 106 PHE cc_start: 0.7602 (t80) cc_final: 0.7152 (t80) REVERT: C 222 LEU cc_start: 0.8388 (tt) cc_final: 0.8065 (mt) REVERT: D 123 VAL cc_start: 0.9222 (p) cc_final: 0.8947 (t) REVERT: D 314 MET cc_start: 0.4606 (ptt) cc_final: 0.4356 (mmt) REVERT: E 9 GLU cc_start: 0.7977 (tt0) cc_final: 0.7681 (mt-10) REVERT: E 306 MET cc_start: 0.8551 (ppp) cc_final: 0.8063 (ptm) outliers start: 36 outliers final: 19 residues processed: 254 average time/residue: 0.2340 time to fit residues: 90.9767 Evaluate side-chains 211 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 596 TRP Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN D 68 HIS E 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15293 Z= 0.251 Angle : 0.676 12.057 20884 Z= 0.333 Chirality : 0.045 0.177 2461 Planarity : 0.004 0.037 2529 Dihedral : 4.925 26.724 2197 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.45 % Allowed : 15.10 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -1.37 (0.20), residues: 1778 helix: 0.84 (0.21), residues: 628 sheet: -1.15 (0.26), residues: 407 loop : -2.33 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 596 HIS 0.007 0.001 HIS C 297 PHE 0.026 0.002 PHE C 355 TYR 0.014 0.001 TYR B 95 ARG 0.004 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 222 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.8526 (p90) cc_final: 0.7993 (p90) REVERT: A 231 ILE cc_start: 0.9010 (pt) cc_final: 0.8789 (mt) REVERT: B 70 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8042 (mtpt) REVERT: B 145 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8929 (p) REVERT: C 106 PHE cc_start: 0.7687 (t80) cc_final: 0.7241 (t80) REVERT: C 222 LEU cc_start: 0.8498 (tt) cc_final: 0.8280 (mt) REVERT: D 123 VAL cc_start: 0.9186 (p) cc_final: 0.8982 (t) REVERT: D 232 SER cc_start: 0.8444 (p) cc_final: 0.8146 (p) outliers start: 58 outliers final: 37 residues processed: 260 average time/residue: 0.2293 time to fit residues: 92.6218 Evaluate side-chains 231 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.0970 chunk 97 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15293 Z= 0.205 Angle : 0.636 13.307 20884 Z= 0.310 Chirality : 0.043 0.171 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.558 20.752 2197 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.03 % Allowed : 18.31 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -1.13 (0.20), residues: 1778 helix: 1.06 (0.21), residues: 630 sheet: -0.97 (0.26), residues: 399 loop : -2.24 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 151 HIS 0.006 0.001 HIS C 297 PHE 0.026 0.001 PHE C 355 TYR 0.014 0.001 TYR B 95 ARG 0.009 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 212 time to evaluate : 1.575 Fit side-chains REVERT: B 70 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8035 (mtpt) REVERT: B 145 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8908 (p) REVERT: C 106 PHE cc_start: 0.7750 (t80) cc_final: 0.7326 (t80) REVERT: C 157 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: C 222 LEU cc_start: 0.8597 (tt) cc_final: 0.8364 (mt) REVERT: C 337 ASP cc_start: 0.4494 (OUTLIER) cc_final: 0.4257 (t0) REVERT: D 123 VAL cc_start: 0.9233 (p) cc_final: 0.8967 (t) REVERT: D 232 SER cc_start: 0.8445 (p) cc_final: 0.8190 (p) REVERT: E 9 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7860 (mt-10) REVERT: E 222 LEU cc_start: 0.8520 (tt) cc_final: 0.8160 (tp) REVERT: E 232 TYR cc_start: 0.8317 (t80) cc_final: 0.7917 (t80) REVERT: E 257 LEU cc_start: 0.8403 (tt) cc_final: 0.8186 (mp) REVERT: E 324 MET cc_start: 0.5838 (tpp) cc_final: 0.5635 (tpp) outliers start: 51 outliers final: 36 residues processed: 251 average time/residue: 0.2294 time to fit residues: 89.7021 Evaluate side-chains 232 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.6980 chunk 154 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15293 Z= 0.176 Angle : 0.619 13.016 20884 Z= 0.300 Chirality : 0.043 0.185 2461 Planarity : 0.004 0.035 2529 Dihedral : 4.396 20.652 2197 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.09 % Allowed : 19.26 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.93 (0.20), residues: 1778 helix: 1.36 (0.21), residues: 603 sheet: -1.06 (0.25), residues: 425 loop : -2.03 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 317 HIS 0.006 0.001 HIS C 297 PHE 0.026 0.001 PHE C 355 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.7736 (t80) cc_final: 0.7342 (t80) REVERT: C 196 TYR cc_start: 0.8239 (t80) cc_final: 0.7979 (t80) REVERT: D 123 VAL cc_start: 0.9241 (p) cc_final: 0.8985 (t) REVERT: D 232 SER cc_start: 0.8576 (p) cc_final: 0.8363 (p) REVERT: D 247 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 199 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8658 (mp) REVERT: E 257 LEU cc_start: 0.8501 (tt) cc_final: 0.8212 (mp) REVERT: E 324 MET cc_start: 0.5841 (tpp) cc_final: 0.5564 (tpp) outliers start: 52 outliers final: 38 residues processed: 241 average time/residue: 0.2244 time to fit residues: 85.0457 Evaluate side-chains 224 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15293 Z= 0.229 Angle : 0.653 13.452 20884 Z= 0.319 Chirality : 0.044 0.179 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.564 22.655 2197 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.69 % Allowed : 19.14 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.87 (0.20), residues: 1778 helix: 1.41 (0.21), residues: 603 sheet: -1.01 (0.25), residues: 426 loop : -2.00 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.006 0.001 HIS C 297 PHE 0.026 0.001 PHE C 355 TYR 0.016 0.001 TYR B 95 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.8675 (p90) cc_final: 0.8246 (p90) REVERT: B 268 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: C 106 PHE cc_start: 0.7747 (t80) cc_final: 0.7306 (t80) REVERT: C 157 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: C 306 MET cc_start: 0.7466 (ttp) cc_final: 0.7144 (ttt) REVERT: C 337 ASP cc_start: 0.4480 (t70) cc_final: 0.4246 (t0) REVERT: D 123 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8972 (t) REVERT: E 199 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8669 (mp) REVERT: E 222 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8106 (mp) REVERT: E 257 LEU cc_start: 0.8560 (tt) cc_final: 0.8263 (mp) REVERT: E 324 MET cc_start: 0.5988 (tpp) cc_final: 0.5774 (tpp) outliers start: 62 outliers final: 48 residues processed: 251 average time/residue: 0.2355 time to fit residues: 91.2837 Evaluate side-chains 242 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 189 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 0.0040 chunk 101 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 155 optimal weight: 0.0980 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15293 Z= 0.158 Angle : 0.614 14.054 20884 Z= 0.295 Chirality : 0.042 0.196 2461 Planarity : 0.004 0.036 2529 Dihedral : 4.328 22.167 2197 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.85 % Allowed : 20.57 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.62 (0.20), residues: 1778 helix: 1.59 (0.21), residues: 603 sheet: -0.86 (0.25), residues: 417 loop : -1.83 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 317 HIS 0.006 0.001 HIS C 297 PHE 0.024 0.001 PHE C 355 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8235 (tt) cc_final: 0.7908 (tt) REVERT: C 106 PHE cc_start: 0.7665 (t80) cc_final: 0.7213 (t80) REVERT: D 123 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.9008 (t) REVERT: E 199 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8613 (mp) REVERT: E 233 LEU cc_start: 0.8615 (tp) cc_final: 0.8195 (tp) REVERT: E 257 LEU cc_start: 0.8511 (tt) cc_final: 0.8225 (mp) outliers start: 48 outliers final: 38 residues processed: 233 average time/residue: 0.2179 time to fit residues: 79.6570 Evaluate side-chains 226 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15293 Z= 0.204 Angle : 0.642 14.069 20884 Z= 0.312 Chirality : 0.043 0.186 2461 Planarity : 0.004 0.035 2529 Dihedral : 4.405 21.980 2197 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.73 % Allowed : 20.69 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.67 (0.20), residues: 1778 helix: 1.52 (0.21), residues: 603 sheet: -0.89 (0.25), residues: 417 loop : -1.84 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 317 HIS 0.006 0.001 HIS B 46 PHE 0.023 0.001 PHE C 355 TYR 0.017 0.001 TYR C 196 ARG 0.004 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 1.875 Fit side-chains REVERT: A 266 ILE cc_start: 0.8354 (tt) cc_final: 0.8070 (tt) REVERT: C 106 PHE cc_start: 0.7560 (t80) cc_final: 0.7166 (t80) REVERT: C 157 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: C 324 MET cc_start: 0.5511 (tpt) cc_final: 0.5099 (tmm) REVERT: D 123 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8985 (t) REVERT: D 312 HIS cc_start: 0.8551 (m170) cc_final: 0.8346 (m90) REVERT: E 199 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8621 (mp) REVERT: E 233 LEU cc_start: 0.8676 (tp) cc_final: 0.8251 (tp) REVERT: E 257 LEU cc_start: 0.8549 (tt) cc_final: 0.8213 (mp) outliers start: 46 outliers final: 41 residues processed: 222 average time/residue: 0.2246 time to fit residues: 78.1977 Evaluate side-chains 229 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.0010 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 149 optimal weight: 0.2980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15293 Z= 0.183 Angle : 0.631 14.564 20884 Z= 0.305 Chirality : 0.043 0.196 2461 Planarity : 0.004 0.034 2529 Dihedral : 4.337 22.687 2197 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.91 % Allowed : 20.69 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.58 (0.20), residues: 1778 helix: 1.63 (0.21), residues: 603 sheet: -0.82 (0.25), residues: 413 loop : -1.82 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 317 HIS 0.006 0.001 HIS B 46 PHE 0.023 0.001 PHE C 355 TYR 0.016 0.001 TYR C 196 ARG 0.003 0.000 ARG D 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: A 266 ILE cc_start: 0.8343 (tt) cc_final: 0.8056 (tt) REVERT: C 106 PHE cc_start: 0.7438 (t80) cc_final: 0.7079 (t80) REVERT: C 324 MET cc_start: 0.5478 (tpt) cc_final: 0.5150 (tmm) REVERT: D 123 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9007 (t) REVERT: D 312 HIS cc_start: 0.8489 (m170) cc_final: 0.8288 (m90) REVERT: E 199 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8600 (mp) REVERT: E 233 LEU cc_start: 0.8627 (tp) cc_final: 0.8223 (tp) REVERT: E 349 PHE cc_start: 0.8502 (m-80) cc_final: 0.8141 (m-80) outliers start: 49 outliers final: 44 residues processed: 232 average time/residue: 0.2243 time to fit residues: 81.1087 Evaluate side-chains 235 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 119 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 58 optimal weight: 0.0020 chunk 144 optimal weight: 0.0170 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3342 r_free = 0.3342 target = 0.126104 restraints weight = 17814.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123803 restraints weight = 26244.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.123103 restraints weight = 18766.186| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15293 Z= 0.157 Angle : 0.614 14.317 20884 Z= 0.295 Chirality : 0.042 0.195 2461 Planarity : 0.004 0.034 2529 Dihedral : 4.182 21.920 2197 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.32 % Allowed : 21.52 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: -0.46 (0.20), residues: 1778 helix: 1.79 (0.21), residues: 601 sheet: -0.77 (0.25), residues: 421 loop : -1.80 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 317 HIS 0.005 0.001 HIS C 297 PHE 0.022 0.001 PHE C 355 TYR 0.016 0.001 TYR C 196 ARG 0.004 0.000 ARG D 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.74 seconds wall clock time: 56 minutes 4.15 seconds (3364.15 seconds total)