Starting phenix.real_space_refine on Sat Jun 29 03:59:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uws_42680/06_2024/8uws_42680.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uws_42680/06_2024/8uws_42680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uws_42680/06_2024/8uws_42680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uws_42680/06_2024/8uws_42680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uws_42680/06_2024/8uws_42680.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uws_42680/06_2024/8uws_42680.pdb" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 4 9.91 5 S 72 5.16 5 C 10981 2.51 5 N 2913 2.21 5 O 3167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C ASP 300": "OD1" <-> "OD2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 480": "OD1" <-> "OD2" Residue "C PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 529": "OD1" <-> "OD2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D ASP 14": "OD1" <-> "OD2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 469": "OD1" <-> "OD2" Residue "D TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 480": "OD1" <-> "OD2" Residue "D TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 499": "OD1" <-> "OD2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 529": "OD1" <-> "OD2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 17137 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4301 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 494} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 4285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4285 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 5, 'PTRANS': 36, 'TRANS': 492} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4264 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 36, 'TRANS': 490} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4283 Classifications: {'peptide': 531} Link IDs: {'PCIS': 5, 'PTRANS': 36, 'TRANS': 489} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.43, per 1000 atoms: 0.55 Number of scatterers: 17137 At special positions: 0 Unit cell: (110.55, 103.18, 113.9, 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 4 19.99 S 72 16.00 O 3167 8.00 N 2913 7.00 C 10981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.53 Conformation dependent library (CDL) restraints added in 2.7 seconds 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 51 sheets defined 1.7% alpha, 53.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 502 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 20 removed outlier: 6.925A pdb=" N ILE C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 132 removed outlier: 5.517A pdb=" N ASP C 127 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 143 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 138 " --> pdb=" O PHE C 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 132 removed outlier: 5.517A pdb=" N ASP C 127 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 143 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 138 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 157 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 186 through 193 removed outlier: 4.886A pdb=" N GLY C 187 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA C 202 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 212 " --> pdb=" O MET C 232 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL C 214 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 230 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N ARG C 216 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 244 through 253 removed outlier: 5.212A pdb=" N LYS C 245 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER C 266 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 249 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 262 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 251 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP C 259 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 331 through 333 Processing sheet with id=AB2, first strand: chain 'C' and resid 331 through 333 removed outlier: 5.678A pdb=" N PHE C 528 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN C 398 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR C 530 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C 396 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR C 473 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR C 475 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 380 through 385 removed outlier: 4.305A pdb=" N SER C 380 " --> pdb=" O CYS C 516 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN C 406 " --> pdb=" O TYR C 426 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR C 426 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 408 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 380 through 385 removed outlier: 4.305A pdb=" N SER C 380 " --> pdb=" O CYS C 516 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN C 406 " --> pdb=" O TYR C 426 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR C 426 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 408 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 453 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AB6, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.928A pdb=" N ILE D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AB8, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 125 through 132 removed outlier: 5.847A pdb=" N ASP D 127 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG D 143 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS D 138 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 168 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 125 through 132 removed outlier: 5.847A pdb=" N ASP D 127 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG D 143 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS D 138 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE D 157 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 186 through 193 removed outlier: 5.190A pdb=" N GLY D 187 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 202 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 212 " --> pdb=" O MET D 232 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL D 214 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 230 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 12.092A pdb=" N ARG D 216 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 244 through 253 removed outlier: 6.758A pdb=" N SER D 246 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER D 266 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS D 248 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU D 264 " --> pdb=" O HIS D 248 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP D 259 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AC6, first strand: chain 'D' and resid 331 through 333 removed outlier: 5.743A pdb=" N PHE D 528 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLN D 398 " --> pdb=" O PHE D 528 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 530 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG D 396 " --> pdb=" O TYR D 530 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR D 473 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR D 475 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 380 through 385 removed outlier: 4.413A pdb=" N SER D 380 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN D 406 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR D 426 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 408 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN D 418 " --> pdb=" O TYR D 414 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 380 through 385 removed outlier: 4.413A pdb=" N SER D 380 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN D 406 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR D 426 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 408 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN D 418 " --> pdb=" O TYR D 414 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AD1, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.876A pdb=" N ILE A 39 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AD3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD4, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'A' and resid 125 through 132 removed outlier: 5.811A pdb=" N ASP A 127 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG A 143 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 138 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 168 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 125 through 132 removed outlier: 5.811A pdb=" N ASP A 127 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG A 143 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 138 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 157 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 186 through 193 removed outlier: 4.055A pdb=" N ALA A 188 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET A 200 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 190 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 198 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A 192 " --> pdb=" O TRP A 196 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 212 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 214 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 230 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N ARG A 216 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 244 through 253 removed outlier: 6.892A pdb=" N SER A 246 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N SER A 266 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS A 248 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 264 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP A 259 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 331 through 333 removed outlier: 5.656A pdb=" N PHE A 528 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN A 398 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 530 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 396 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 356 through 357 removed outlier: 5.656A pdb=" N PHE A 528 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN A 398 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 530 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 396 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 380 through 385 removed outlier: 4.265A pdb=" N SER A 380 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A 406 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR A 426 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 408 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 380 through 385 removed outlier: 4.265A pdb=" N SER A 380 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A 406 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR A 426 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 408 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AE5, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.912A pdb=" N ILE B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AE7, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AE8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AE9, first strand: chain 'B' and resid 125 through 132 removed outlier: 5.795A pdb=" N ASP B 127 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG B 143 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 138 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 157 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 186 through 193 removed outlier: 4.078A pdb=" N ALA B 188 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET B 200 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 190 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR B 198 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG B 192 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 212 " --> pdb=" O MET B 232 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 214 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 230 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ARG B 216 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 244 through 253 removed outlier: 6.667A pdb=" N SER B 246 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N SER B 266 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N HIS B 248 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 264 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP B 259 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AF4, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.746A pdb=" N PHE B 528 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN B 398 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR B 530 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG B 396 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR B 473 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 475 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 380 through 385 removed outlier: 4.294A pdb=" N SER B 380 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 406 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 426 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 408 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 418 " --> pdb=" O TYR B 414 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 380 through 385 removed outlier: 4.294A pdb=" N SER B 380 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 406 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 426 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 408 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 418 " --> pdb=" O TYR B 414 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 6.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3987 1.33 - 1.45: 4445 1.45 - 1.57: 9194 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 17738 Sorted by residual: bond pdb=" CA TRP C 331 " pdb=" C TRP C 331 " ideal model delta sigma weight residual 1.524 1.444 0.079 1.31e-02 5.83e+03 3.64e+01 bond pdb=" CA GLU C 322 " pdb=" C GLU C 322 " ideal model delta sigma weight residual 1.523 1.446 0.078 1.30e-02 5.92e+03 3.57e+01 bond pdb=" CA TYR D 500 " pdb=" C TYR D 500 " ideal model delta sigma weight residual 1.521 1.473 0.048 9.90e-03 1.02e+04 2.33e+01 bond pdb=" CA HIS C 227 " pdb=" C HIS C 227 " ideal model delta sigma weight residual 1.527 1.468 0.060 1.25e-02 6.40e+03 2.29e+01 bond pdb=" CA PHE A 506 " pdb=" C PHE A 506 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.34e-02 5.57e+03 1.93e+01 ... (remaining 17733 not shown) Histogram of bond angle deviations from ideal: 97.54 - 104.96: 491 104.96 - 112.39: 8551 112.39 - 119.81: 6305 119.81 - 127.23: 8500 127.23 - 134.65: 387 Bond angle restraints: 24234 Sorted by residual: angle pdb=" N SER C 330 " pdb=" CA SER C 330 " pdb=" C SER C 330 " ideal model delta sigma weight residual 110.80 97.54 13.26 2.13e+00 2.20e-01 3.87e+01 angle pdb=" N ARG C 504 " pdb=" CA ARG C 504 " pdb=" C ARG C 504 " ideal model delta sigma weight residual 113.30 105.25 8.05 1.34e+00 5.57e-01 3.61e+01 angle pdb=" N THR A 4 " pdb=" CA THR A 4 " pdb=" C THR A 4 " ideal model delta sigma weight residual 107.73 117.78 -10.05 1.80e+00 3.09e-01 3.12e+01 angle pdb=" N GLN C 323 " pdb=" CA GLN C 323 " pdb=" C GLN C 323 " ideal model delta sigma weight residual 109.84 102.63 7.21 1.39e+00 5.18e-01 2.69e+01 angle pdb=" N ARG B 504 " pdb=" CA ARG B 504 " pdb=" C ARG B 504 " ideal model delta sigma weight residual 112.88 106.41 6.47 1.29e+00 6.01e-01 2.52e+01 ... (remaining 24229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8856 17.95 - 35.91: 972 35.91 - 53.86: 264 53.86 - 71.81: 53 71.81 - 89.76: 27 Dihedral angle restraints: 10172 sinusoidal: 4052 harmonic: 6120 Sorted by residual: dihedral pdb=" CA THR A 219 " pdb=" C THR A 219 " pdb=" N ILE A 220 " pdb=" CA ILE A 220 " ideal model delta harmonic sigma weight residual 180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP C 127 " pdb=" CB ASP C 127 " pdb=" CG ASP C 127 " pdb=" OD1 ASP C 127 " ideal model delta sinusoidal sigma weight residual -30.00 -94.13 64.13 1 2.00e+01 2.50e-03 1.35e+01 dihedral pdb=" CA CYS D 412 " pdb=" C CYS D 412 " pdb=" N TYR D 413 " pdb=" CA TYR D 413 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 10169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2224 0.085 - 0.170: 222 0.170 - 0.255: 11 0.255 - 0.339: 0 0.339 - 0.424: 3 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA CYS C 183 " pdb=" N CYS C 183 " pdb=" C CYS C 183 " pdb=" CB CYS C 183 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA CYS D 183 " pdb=" N CYS D 183 " pdb=" C CYS D 183 " pdb=" CB CYS D 183 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA CYS B 183 " pdb=" N CYS B 183 " pdb=" C CYS B 183 " pdb=" CB CYS B 183 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 2457 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 501 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ILE C 501 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE C 501 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY C 502 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 499 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C ASP D 499 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP D 499 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR D 500 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 501 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ILE B 501 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE B 501 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY B 502 " 0.016 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 3 2.24 - 2.91: 7012 2.91 - 3.57: 21468 3.57 - 4.24: 41783 4.24 - 4.90: 72702 Nonbonded interactions: 142968 Sorted by model distance: nonbonded pdb=" ND1 HIS D 227 " pdb=" CD PRO D 228 " model vdw 1.576 3.520 nonbonded pdb=" O ASN B 155 " pdb=" ND2 ASN B 155 " model vdw 2.236 2.520 nonbonded pdb=" O ASN A 155 " pdb=" ND2 ASN A 155 " model vdw 2.240 2.520 nonbonded pdb=" O ASN C 155 " pdb=" ND2 ASN C 155 " model vdw 2.241 2.520 nonbonded pdb=" OD2 ASP C 68 " pdb=" OG SER C 416 " model vdw 2.242 2.440 ... (remaining 142963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 324 or resid 330 through 427 or (resid 428 and ( \ name N or name CA or name C or name O or name CB )) or resid 429 through 457 or \ (resid 458 through 459 and (name N or name CA or name C or name O or name CB )) \ or resid 460 through 536 or resid 601)) selection = (chain 'B' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 164 or (resid 165 and (name N or \ name CA or name C or name O or name CB )) or resid 166 through 427 or (resid 42 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 429 through \ 449 or (resid 450 through 451 and (name N or name CA or name C or name O or name \ CB )) or resid 452 through 457 or (resid 458 through 459 and (name N or name CA \ or name C or name O or name CB )) or resid 460 through 481 or (resid 482 and (n \ ame N or name CA or name C or name O or name CB )) or resid 483 through 533 or ( \ resid 534 and (name N or name CA or name C or name O or name CB )) or resid 535 \ through 536 or resid 601)) selection = (chain 'C' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 164 or (resid 165 and (name N or \ name CA or name C or name O or name CB )) or resid 166 through 324 or resid 330 \ through 427 or (resid 428 and (name N or name CA or name C or name O or name CB \ )) or resid 429 through 481 or (resid 482 and (name N or name CA or name C or n \ ame O or name CB )) or resid 483 through 533 or (resid 534 and (name N or name C \ A or name C or name O or name CB )) or resid 535 through 536 or resid 601)) selection = (chain 'D' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 324 or resid 330 through 449 or \ (resid 450 through 451 and (name N or name CA or name C or name O or name CB )) \ or resid 452 through 457 or (resid 458 through 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 533 or (resid 534 and (name N o \ r name CA or name C or name O or name CB )) or resid 535 through 536 or resid 60 \ 1)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.120 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.070 Find NCS groups from input model: 1.260 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.005 0.079 17738 Z= 0.340 Angle : 0.728 13.259 24234 Z= 0.417 Chirality : 0.050 0.424 2460 Planarity : 0.005 0.063 3155 Dihedral : 16.680 89.763 6302 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.53 % Favored : 95.19 % Rotamer: Outliers : 2.74 % Allowed : 24.31 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.72 (0.18), residues: 2119 helix: -4.02 (0.64), residues: 24 sheet: 0.67 (0.19), residues: 776 loop : -1.19 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 48 HIS 0.010 0.001 HIS C 227 PHE 0.034 0.002 PHE B 506 TYR 0.021 0.002 TYR B 79 ARG 0.010 0.001 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 497 time to evaluate : 2.046 Fit side-chains REVERT: C 192 ARG cc_start: 0.7991 (ttt90) cc_final: 0.7787 (ttt90) REVERT: C 206 THR cc_start: 0.8327 (t) cc_final: 0.7997 (m) REVERT: D 178 THR cc_start: 0.8138 (p) cc_final: 0.7926 (m) REVERT: D 192 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7609 (ttt90) REVERT: D 206 THR cc_start: 0.8319 (t) cc_final: 0.7960 (m) REVERT: D 330 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7644 (p) REVERT: A 391 PHE cc_start: 0.8221 (p90) cc_final: 0.7912 (p90) REVERT: A 506 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7816 (p90) REVERT: B 206 THR cc_start: 0.8340 (t) cc_final: 0.7989 (m) REVERT: B 438 GLN cc_start: 0.8325 (tt0) cc_final: 0.8045 (tt0) outliers start: 50 outliers final: 24 residues processed: 523 average time/residue: 1.1022 time to fit residues: 649.7609 Evaluate side-chains 503 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 477 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 446 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 101 optimal weight: 0.0270 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 HIS D 155 ASN D 515 HIS A 5 ASN A 160 GLN A 398 GLN A 406 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 160 GLN B 323 GLN B 398 GLN B 403 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17738 Z= 0.306 Angle : 0.606 6.813 24234 Z= 0.313 Chirality : 0.047 0.179 2460 Planarity : 0.005 0.065 3155 Dihedral : 5.992 57.176 2415 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 5.60 % Allowed : 20.47 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.50 (0.18), residues: 2119 helix: -3.64 (0.61), residues: 36 sheet: 0.98 (0.19), residues: 754 loop : -1.08 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 298 HIS 0.007 0.001 HIS B 403 PHE 0.015 0.002 PHE D 84 TYR 0.020 0.002 TYR D 413 ARG 0.007 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 481 time to evaluate : 1.960 Fit side-chains REVERT: C 64 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8018 (ttpp) REVERT: C 192 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7799 (ttt180) REVERT: C 265 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7671 (t) REVERT: C 445 SER cc_start: 0.8473 (t) cc_final: 0.8187 (m) REVERT: D 102 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6839 (mtt-85) REVERT: D 206 THR cc_start: 0.8298 (t) cc_final: 0.7913 (m) REVERT: D 438 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: A 4 THR cc_start: 0.8314 (m) cc_final: 0.8104 (t) REVERT: A 497 SER cc_start: 0.7993 (p) cc_final: 0.7625 (p) REVERT: A 507 PHE cc_start: 0.7892 (m-10) cc_final: 0.7624 (m-80) REVERT: B 32 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7295 (pm20) REVERT: B 152 ASN cc_start: 0.8512 (p0) cc_final: 0.8282 (p0) REVERT: B 507 PHE cc_start: 0.7721 (m-80) cc_final: 0.7386 (m-80) outliers start: 102 outliers final: 50 residues processed: 527 average time/residue: 1.0973 time to fit residues: 653.3304 Evaluate side-chains 517 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 462 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 171 optimal weight: 0.3980 chunk 191 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 ASN D 312 GLN D 515 HIS A 160 GLN A 398 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 398 GLN B 403 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17738 Z= 0.255 Angle : 0.575 8.212 24234 Z= 0.296 Chirality : 0.045 0.167 2460 Planarity : 0.005 0.051 3155 Dihedral : 5.122 57.349 2385 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.06 % Favored : 95.71 % Rotamer: Outliers : 5.27 % Allowed : 21.19 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.40 (0.18), residues: 2119 helix: -3.76 (0.53), residues: 36 sheet: 1.10 (0.19), residues: 761 loop : -1.06 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 98 HIS 0.007 0.001 HIS B 403 PHE 0.014 0.002 PHE A 391 TYR 0.022 0.001 TYR B 413 ARG 0.004 0.000 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 476 time to evaluate : 1.886 Fit side-chains REVERT: C 192 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7839 (ttt90) REVERT: C 201 VAL cc_start: 0.8426 (m) cc_final: 0.8113 (t) REVERT: C 445 SER cc_start: 0.8476 (t) cc_final: 0.8201 (m) REVERT: D 102 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6798 (mtt-85) REVERT: D 143 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.6850 (ttt-90) REVERT: D 206 THR cc_start: 0.8244 (t) cc_final: 0.7912 (m) REVERT: D 438 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: A 95 ASP cc_start: 0.7647 (t0) cc_final: 0.7389 (t0) REVERT: A 102 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6830 (mtt-85) REVERT: A 407 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8255 (m) REVERT: A 497 SER cc_start: 0.7982 (p) cc_final: 0.7611 (p) REVERT: A 507 PHE cc_start: 0.7946 (m-10) cc_final: 0.7618 (m-80) REVERT: B 152 ASN cc_start: 0.8484 (p0) cc_final: 0.8238 (p0) REVERT: B 322 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6633 (mt-10) REVERT: B 507 PHE cc_start: 0.7777 (m-80) cc_final: 0.7387 (m-80) outliers start: 96 outliers final: 63 residues processed: 522 average time/residue: 1.0635 time to fit residues: 628.1370 Evaluate side-chains 535 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 467 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 193 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 101 optimal weight: 0.0170 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 398 GLN D 155 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 323 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17738 Z= 0.200 Angle : 0.547 7.586 24234 Z= 0.282 Chirality : 0.044 0.167 2460 Planarity : 0.005 0.048 3155 Dihedral : 4.774 56.636 2380 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.01 % Favored : 95.75 % Rotamer: Outliers : 4.94 % Allowed : 21.57 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.28 (0.18), residues: 2119 helix: -3.72 (0.49), residues: 36 sheet: 1.19 (0.19), residues: 759 loop : -0.98 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 48 HIS 0.007 0.001 HIS B 403 PHE 0.012 0.001 PHE A 391 TYR 0.025 0.001 TYR D 413 ARG 0.005 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 462 time to evaluate : 1.859 Fit side-chains REVERT: C 4 THR cc_start: 0.8292 (m) cc_final: 0.8085 (p) REVERT: C 64 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7951 (tttp) REVERT: C 192 ARG cc_start: 0.8012 (ttt90) cc_final: 0.7807 (ttt180) REVERT: C 206 THR cc_start: 0.8265 (t) cc_final: 0.7958 (m) REVERT: C 445 SER cc_start: 0.8463 (t) cc_final: 0.8187 (m) REVERT: D 102 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6774 (mtt-85) REVERT: D 143 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.6691 (ttt-90) REVERT: D 206 THR cc_start: 0.8193 (t) cc_final: 0.7917 (m) REVERT: A 95 ASP cc_start: 0.7646 (t0) cc_final: 0.7390 (t0) REVERT: A 102 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6833 (mtt-85) REVERT: A 497 SER cc_start: 0.7951 (p) cc_final: 0.7681 (p) REVERT: A 507 PHE cc_start: 0.7955 (m-10) cc_final: 0.7601 (m-80) REVERT: B 152 ASN cc_start: 0.8463 (p0) cc_final: 0.8242 (p0) REVERT: B 507 PHE cc_start: 0.7775 (m-80) cc_final: 0.7390 (m-80) outliers start: 90 outliers final: 58 residues processed: 499 average time/residue: 1.0833 time to fit residues: 611.2923 Evaluate side-chains 515 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 453 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 499 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 0.4980 chunk 141 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN D 155 ASN D 403 HIS D 515 HIS A 100 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 403 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17738 Z= 0.231 Angle : 0.561 7.279 24234 Z= 0.289 Chirality : 0.045 0.170 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.668 56.506 2377 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.06 % Favored : 95.71 % Rotamer: Outliers : 5.05 % Allowed : 22.12 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.26 (0.18), residues: 2119 helix: -3.52 (0.50), residues: 36 sheet: 1.24 (0.19), residues: 766 loop : -1.01 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 463 HIS 0.007 0.001 HIS D 403 PHE 0.011 0.001 PHE B 126 TYR 0.024 0.001 TYR D 413 ARG 0.006 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 458 time to evaluate : 2.265 Fit side-chains REVERT: C 4 THR cc_start: 0.8304 (m) cc_final: 0.8094 (p) REVERT: C 64 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7965 (tttp) REVERT: C 192 ARG cc_start: 0.8018 (ttt90) cc_final: 0.7817 (ttt180) REVERT: C 206 THR cc_start: 0.8245 (t) cc_final: 0.7956 (m) REVERT: D 102 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6759 (mtt-85) REVERT: D 143 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.6924 (ttt-90) REVERT: D 206 THR cc_start: 0.8216 (t) cc_final: 0.7943 (m) REVERT: D 438 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: A 86 LEU cc_start: 0.8529 (tp) cc_final: 0.8285 (tt) REVERT: A 95 ASP cc_start: 0.7662 (t0) cc_final: 0.7397 (t0) REVERT: A 102 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6834 (mtt-85) REVERT: A 497 SER cc_start: 0.7997 (p) cc_final: 0.7736 (p) REVERT: A 507 PHE cc_start: 0.7970 (m-10) cc_final: 0.7668 (m-80) REVERT: B 152 ASN cc_start: 0.8466 (p0) cc_final: 0.8240 (p0) REVERT: B 206 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7981 (m) REVERT: B 507 PHE cc_start: 0.7797 (m-80) cc_final: 0.7409 (m-80) outliers start: 92 outliers final: 59 residues processed: 497 average time/residue: 1.0548 time to fit residues: 594.1588 Evaluate side-chains 516 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 451 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.1980 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 370 ASN D 155 ASN D 403 HIS A 100 ASN A 155 ASN A 398 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 398 GLN B 403 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17738 Z= 0.254 Angle : 0.566 7.264 24234 Z= 0.291 Chirality : 0.045 0.185 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.633 53.622 2375 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.11 % Favored : 95.66 % Rotamer: Outliers : 5.65 % Allowed : 21.90 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.24 (0.18), residues: 2119 helix: -3.47 (0.50), residues: 36 sheet: 1.26 (0.19), residues: 766 loop : -1.01 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 PHE 0.011 0.001 PHE B 126 TYR 0.023 0.002 TYR D 413 ARG 0.005 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 458 time to evaluate : 1.875 Fit side-chains REVERT: C 4 THR cc_start: 0.8300 (m) cc_final: 0.8100 (p) REVERT: C 32 GLU cc_start: 0.7799 (pm20) cc_final: 0.7551 (pm20) REVERT: C 64 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7958 (tttp) REVERT: C 206 THR cc_start: 0.8234 (t) cc_final: 0.7971 (m) REVERT: D 102 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6763 (mtt-85) REVERT: D 143 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.6874 (ttt-90) REVERT: D 206 THR cc_start: 0.8189 (t) cc_final: 0.7945 (m) REVERT: D 438 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: A 86 LEU cc_start: 0.8536 (tp) cc_final: 0.8290 (tt) REVERT: A 95 ASP cc_start: 0.7649 (t0) cc_final: 0.7421 (t0) REVERT: A 102 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6858 (mtt-85) REVERT: A 206 THR cc_start: 0.8202 (t) cc_final: 0.7961 (m) REVERT: A 497 SER cc_start: 0.8035 (p) cc_final: 0.7750 (p) REVERT: A 507 PHE cc_start: 0.7944 (m-10) cc_final: 0.7654 (m-80) REVERT: B 152 ASN cc_start: 0.8471 (p0) cc_final: 0.8239 (p0) REVERT: B 206 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7989 (m) REVERT: B 507 PHE cc_start: 0.7802 (m-80) cc_final: 0.7401 (m-80) outliers start: 103 outliers final: 66 residues processed: 504 average time/residue: 1.0515 time to fit residues: 601.2262 Evaluate side-chains 523 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 451 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 398 GLN D 155 ASN D 403 HIS A 100 ASN A 155 ASN A 398 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 398 GLN B 403 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17738 Z= 0.323 Angle : 0.595 7.706 24234 Z= 0.304 Chirality : 0.046 0.188 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.717 53.696 2375 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.34 % Favored : 95.42 % Rotamer: Outliers : 5.16 % Allowed : 22.45 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.27 (0.18), residues: 2119 helix: -3.33 (0.54), residues: 36 sheet: 1.24 (0.19), residues: 764 loop : -1.03 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 463 HIS 0.007 0.001 HIS B 403 PHE 0.012 0.002 PHE A 423 TYR 0.022 0.002 TYR D 413 ARG 0.006 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 470 time to evaluate : 1.834 Fit side-chains REVERT: C 4 THR cc_start: 0.8297 (m) cc_final: 0.8091 (p) REVERT: C 32 GLU cc_start: 0.7809 (pm20) cc_final: 0.7531 (pm20) REVERT: C 64 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7974 (tttp) REVERT: C 206 THR cc_start: 0.8236 (t) cc_final: 0.7978 (m) REVERT: D 102 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6771 (mtt-85) REVERT: D 143 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.6982 (ttt-90) REVERT: D 185 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7654 (t) REVERT: D 206 THR cc_start: 0.8198 (t) cc_final: 0.7957 (m) REVERT: D 438 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: A 86 LEU cc_start: 0.8535 (tp) cc_final: 0.8289 (tt) REVERT: A 95 ASP cc_start: 0.7653 (t0) cc_final: 0.7429 (t0) REVERT: A 102 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6813 (mtt-85) REVERT: A 206 THR cc_start: 0.8177 (t) cc_final: 0.7961 (m) REVERT: A 238 LEU cc_start: 0.7943 (mt) cc_final: 0.7730 (mt) REVERT: A 497 SER cc_start: 0.8048 (p) cc_final: 0.7778 (p) REVERT: A 507 PHE cc_start: 0.7938 (m-10) cc_final: 0.7646 (m-80) REVERT: B 152 ASN cc_start: 0.8482 (p0) cc_final: 0.8237 (p0) REVERT: B 206 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8001 (m) REVERT: B 507 PHE cc_start: 0.7827 (m-80) cc_final: 0.7390 (m-80) outliers start: 94 outliers final: 61 residues processed: 510 average time/residue: 1.0920 time to fit residues: 630.2558 Evaluate side-chains 532 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 464 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 0.1980 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 160 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 398 GLN D 155 ASN D 403 HIS A 100 ASN A 155 ASN A 398 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 398 GLN B 403 HIS B 406 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17738 Z= 0.170 Angle : 0.539 7.025 24234 Z= 0.279 Chirality : 0.044 0.169 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.512 51.634 2375 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.11 % Favored : 95.66 % Rotamer: Outliers : 4.56 % Allowed : 23.16 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.16 (0.18), residues: 2119 helix: -2.51 (0.74), residues: 30 sheet: 1.26 (0.19), residues: 777 loop : -0.97 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 PHE 0.010 0.001 PHE A 391 TYR 0.027 0.001 TYR D 413 ARG 0.005 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 476 time to evaluate : 1.737 Fit side-chains REVERT: C 32 GLU cc_start: 0.7800 (pm20) cc_final: 0.7567 (pm20) REVERT: C 64 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7876 (tttp) REVERT: C 206 THR cc_start: 0.8204 (t) cc_final: 0.7953 (m) REVERT: C 265 THR cc_start: 0.7757 (t) cc_final: 0.7549 (t) REVERT: C 440 ASP cc_start: 0.7978 (t0) cc_final: 0.7582 (p0) REVERT: D 57 ARG cc_start: 0.8164 (ptt90) cc_final: 0.7555 (ptt90) REVERT: D 102 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6762 (mtt-85) REVERT: D 143 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.6883 (ttt-90) REVERT: D 438 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: D 507 PHE cc_start: 0.7516 (m-80) cc_final: 0.7307 (m-80) REVERT: A 86 LEU cc_start: 0.8513 (tp) cc_final: 0.8269 (tt) REVERT: A 95 ASP cc_start: 0.7646 (t0) cc_final: 0.7406 (t0) REVERT: A 102 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6816 (mtt-85) REVERT: A 206 THR cc_start: 0.8135 (t) cc_final: 0.7927 (m) REVERT: A 370 ASN cc_start: 0.8246 (m-40) cc_final: 0.7997 (m110) REVERT: A 497 SER cc_start: 0.8073 (p) cc_final: 0.7799 (p) REVERT: A 507 PHE cc_start: 0.7903 (m-10) cc_final: 0.7622 (m-80) REVERT: B 152 ASN cc_start: 0.8461 (p0) cc_final: 0.8226 (p0) REVERT: B 206 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8000 (m) REVERT: B 507 PHE cc_start: 0.7794 (m-80) cc_final: 0.7405 (m-80) outliers start: 83 outliers final: 49 residues processed: 508 average time/residue: 1.0539 time to fit residues: 606.6244 Evaluate side-chains 519 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 464 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 189 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 398 GLN D 155 ASN D 403 HIS D 418 ASN A 100 ASN A 155 ASN A 398 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 398 GLN B 403 HIS B 406 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17738 Z= 0.342 Angle : 0.606 7.789 24234 Z= 0.310 Chirality : 0.047 0.183 2460 Planarity : 0.005 0.048 3155 Dihedral : 4.473 20.006 2370 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.67 % Favored : 95.09 % Rotamer: Outliers : 4.56 % Allowed : 24.09 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.24 (0.18), residues: 2119 helix: -3.01 (0.62), residues: 36 sheet: 1.25 (0.19), residues: 766 loop : -1.01 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 48 HIS 0.008 0.001 HIS B 403 PHE 0.013 0.002 PHE A 423 TYR 0.024 0.002 TYR D 413 ARG 0.007 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 477 time to evaluate : 1.873 Fit side-chains REVERT: C 32 GLU cc_start: 0.7806 (pm20) cc_final: 0.7546 (pm20) REVERT: C 64 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7962 (tttp) REVERT: C 206 THR cc_start: 0.8232 (t) cc_final: 0.7980 (m) REVERT: D 57 ARG cc_start: 0.8205 (ptt90) cc_final: 0.7612 (ptt90) REVERT: D 95 ASP cc_start: 0.7465 (t0) cc_final: 0.7190 (t0) REVERT: D 102 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6759 (mtt-85) REVERT: D 143 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.6985 (ttt-90) REVERT: D 185 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7636 (t) REVERT: D 438 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: A 86 LEU cc_start: 0.8539 (tp) cc_final: 0.8296 (tt) REVERT: A 95 ASP cc_start: 0.7662 (t0) cc_final: 0.7420 (t0) REVERT: A 102 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6819 (mtt-85) REVERT: A 238 LEU cc_start: 0.7939 (mt) cc_final: 0.7724 (mt) REVERT: A 497 SER cc_start: 0.8064 (p) cc_final: 0.7789 (p) REVERT: A 507 PHE cc_start: 0.7907 (m-10) cc_final: 0.7647 (m-80) REVERT: B 152 ASN cc_start: 0.8493 (p0) cc_final: 0.8247 (p0) REVERT: B 206 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.8013 (m) REVERT: B 507 PHE cc_start: 0.7834 (m-80) cc_final: 0.7375 (m-80) outliers start: 83 outliers final: 54 residues processed: 514 average time/residue: 1.0467 time to fit residues: 610.0408 Evaluate side-chains 531 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 470 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 0.0170 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 155 ASN C 398 GLN D 403 HIS A 100 ASN A 155 ASN A 398 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 398 GLN B 403 HIS B 406 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17738 Z= 0.218 Angle : 0.568 7.285 24234 Z= 0.294 Chirality : 0.045 0.185 2460 Planarity : 0.005 0.045 3155 Dihedral : 4.399 19.988 2370 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.34 % Favored : 95.42 % Rotamer: Outliers : 3.95 % Allowed : 25.30 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.20 (0.18), residues: 2119 helix: -2.79 (0.67), residues: 36 sheet: 1.27 (0.19), residues: 766 loop : -0.98 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 PHE 0.011 0.001 PHE A 391 TYR 0.028 0.001 TYR D 413 ARG 0.007 0.000 ARG A 474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 468 time to evaluate : 1.864 Fit side-chains REVERT: C 32 GLU cc_start: 0.7806 (pm20) cc_final: 0.7573 (pm20) REVERT: C 206 THR cc_start: 0.8201 (t) cc_final: 0.7968 (m) REVERT: C 440 ASP cc_start: 0.7967 (t0) cc_final: 0.7685 (p0) REVERT: D 57 ARG cc_start: 0.8188 (ptt90) cc_final: 0.7608 (ptt90) REVERT: D 95 ASP cc_start: 0.7467 (t0) cc_final: 0.7183 (t0) REVERT: D 102 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6752 (mtt-85) REVERT: D 143 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6902 (ttt-90) REVERT: D 185 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7645 (m) REVERT: D 438 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: A 4 THR cc_start: 0.8286 (t) cc_final: 0.8063 (p) REVERT: A 86 LEU cc_start: 0.8533 (tp) cc_final: 0.8289 (tt) REVERT: A 95 ASP cc_start: 0.7649 (t0) cc_final: 0.7416 (t0) REVERT: A 102 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6813 (mtt-85) REVERT: A 497 SER cc_start: 0.8060 (p) cc_final: 0.7791 (p) REVERT: A 507 PHE cc_start: 0.7862 (m-10) cc_final: 0.7598 (m-80) REVERT: B 152 ASN cc_start: 0.8477 (p0) cc_final: 0.8254 (p0) REVERT: B 206 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.8008 (m) REVERT: B 507 PHE cc_start: 0.7813 (m-80) cc_final: 0.7391 (m-80) outliers start: 72 outliers final: 49 residues processed: 495 average time/residue: 1.0563 time to fit residues: 593.9253 Evaluate side-chains 525 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 470 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 323 GLN C 398 GLN D 155 ASN D 403 HIS A 100 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 398 GLN B 403 HIS B 406 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108895 restraints weight = 23629.822| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.71 r_work: 0.3429 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17738 Z= 0.307 Angle : 0.601 7.828 24234 Z= 0.309 Chirality : 0.046 0.227 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.493 21.459 2370 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.28 % Rotamer: Outliers : 3.95 % Allowed : 25.36 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % 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: -0.23 (0.18), residues: 2119 helix: -2.79 (0.67), residues: 36 sheet: 1.26 (0.19), residues: 766 loop : -1.01 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 48 HIS 0.007 0.001 HIS B 403 PHE 0.013 0.002 PHE D 506 TYR 0.024 0.002 TYR D 413 ARG 0.007 0.000 ARG A 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8690.84 seconds wall clock time: 151 minutes 13.82 seconds (9073.82 seconds total)