Starting phenix.real_space_refine on Wed Feb 21 00:45:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8d_35248/02_2024/8i8d_35248_neut_updated.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.089 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 P 12 5.49 5 S 120 5.16 5 C 18564 2.51 5 N 4824 2.21 5 O 5610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 309": "OE1" <-> "OE2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "f ASP 51": "OD1" <-> "OD2" Residue "f ASP 56": "OD1" <-> "OD2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "b ASP 51": "OD1" <-> "OD2" Residue "b ASP 56": "OD1" <-> "OD2" Residue "c ASP 51": "OD1" <-> "OD2" Residue "c ASP 56": "OD1" <-> "OD2" Residue "d ASP 51": "OD1" <-> "OD2" Residue "d ASP 56": "OD1" <-> "OD2" Residue "e ASP 51": "OD1" <-> "OD2" Residue "e ASP 56": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29130 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4218 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4218 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4218 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4218 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4218 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4218 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 581 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 581 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "b" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 581 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "c" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 581 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "d" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 581 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "e" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 581 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'OP3': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.02, per 1000 atoms: 0.52 Number of scatterers: 29130 At special positions: 0 Unit cell: (183.534, 167.31, 86.19, 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) S 120 16.00 P 12 15.00 O 5610 8.00 N 4824 7.00 C 18564 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.56 Conformation dependent library (CDL) restraints added in 4.9 seconds 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 42 sheets defined 37.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.631A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 118 through 126 Proline residue: A 122 - end of helix removed outlier: 3.549A pdb=" N GLN A 126 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.778A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 227 through 239 Proline residue: A 233 - end of helix removed outlier: 3.563A pdb=" N ALA A 236 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 237 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.998A pdb=" N ARG A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.707A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 41 through 57 Processing helix chain 'B' and resid 74 through 85 removed outlier: 3.631A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 126 Proline residue: B 122 - end of helix removed outlier: 3.549A pdb=" N GLN B 126 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.777A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 227 through 239 Proline residue: B 233 - end of helix removed outlier: 3.563A pdb=" N ALA B 236 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 237 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.998A pdb=" N ARG B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 440 through 448 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.708A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 504 No H-bonds generated for 'chain 'B' and resid 502 through 504' Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 41 through 57 Processing helix chain 'C' and resid 74 through 85 removed outlier: 3.631A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 118 through 126 Proline residue: C 122 - end of helix removed outlier: 3.550A pdb=" N GLN C 126 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 147 through 154 removed outlier: 3.777A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 227 through 239 Proline residue: C 233 - end of helix removed outlier: 3.564A pdb=" N ALA C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 237 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.997A pdb=" N ARG C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 440 through 448 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.708A pdb=" N PHE C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 504 No H-bonds generated for 'chain 'C' and resid 502 through 504' Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 74 through 85 removed outlier: 3.631A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 118 through 126 Proline residue: D 122 - end of helix removed outlier: 3.550A pdb=" N GLN D 126 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.778A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 227 through 239 Proline residue: D 233 - end of helix removed outlier: 3.563A pdb=" N ALA D 236 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 237 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.998A pdb=" N ARG D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 341 through 348 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 484 through 497 removed outlier: 3.707A pdb=" N PHE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'D' and resid 525 through 531 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 41 through 57 Processing helix chain 'E' and resid 74 through 85 removed outlier: 3.631A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 118 through 126 Proline residue: E 122 - end of helix removed outlier: 3.549A pdb=" N GLN E 126 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 147 through 154 removed outlier: 3.777A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 227 through 239 Proline residue: E 233 - end of helix removed outlier: 3.563A pdb=" N ALA E 236 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR E 237 " --> pdb=" O TYR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 310 removed outlier: 3.998A pdb=" N ARG E 310 " --> pdb=" O SER E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 341 through 348 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 484 through 497 removed outlier: 3.708A pdb=" N PHE E 494 " --> pdb=" O PHE E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 504 No H-bonds generated for 'chain 'E' and resid 502 through 504' Processing helix chain 'E' and resid 525 through 531 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 41 through 57 Processing helix chain 'F' and resid 74 through 85 removed outlier: 3.631A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 118 through 126 Proline residue: F 122 - end of helix removed outlier: 3.549A pdb=" N GLN F 126 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 147 through 154 removed outlier: 3.777A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 227 through 239 Proline residue: F 233 - end of helix removed outlier: 3.563A pdb=" N ALA F 236 " --> pdb=" O PRO F 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR F 237 " --> pdb=" O TYR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 270 through 278 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 301 through 310 removed outlier: 3.998A pdb=" N ARG F 310 " --> pdb=" O SER F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 341 through 348 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 440 through 448 Processing helix chain 'F' and resid 484 through 497 removed outlier: 3.707A pdb=" N PHE F 494 " --> pdb=" O PHE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 504 No H-bonds generated for 'chain 'F' and resid 502 through 504' Processing helix chain 'F' and resid 525 through 531 Processing helix chain 'f' and resid 3 through 15 Processing helix chain 'f' and resid 19 through 21 No H-bonds generated for 'chain 'f' and resid 19 through 21' Processing helix chain 'f' and resid 36 through 50 Processing helix chain 'f' and resid 56 through 61 removed outlier: 3.650A pdb=" N LYS f 61 " --> pdb=" O GLU f 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 73 Processing helix chain 'a' and resid 3 through 15 Processing helix chain 'a' and resid 19 through 21 No H-bonds generated for 'chain 'a' and resid 19 through 21' Processing helix chain 'a' and resid 36 through 50 Processing helix chain 'a' and resid 56 through 61 removed outlier: 3.649A pdb=" N LYS a 61 " --> pdb=" O GLU a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 73 Processing helix chain 'b' and resid 3 through 15 Processing helix chain 'b' and resid 19 through 21 No H-bonds generated for 'chain 'b' and resid 19 through 21' Processing helix chain 'b' and resid 36 through 50 Processing helix chain 'b' and resid 56 through 61 removed outlier: 3.649A pdb=" N LYS b 61 " --> pdb=" O GLU b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 73 Processing helix chain 'c' and resid 3 through 15 Processing helix chain 'c' and resid 19 through 21 No H-bonds generated for 'chain 'c' and resid 19 through 21' Processing helix chain 'c' and resid 36 through 50 Processing helix chain 'c' and resid 56 through 61 removed outlier: 3.649A pdb=" N LYS c 61 " --> pdb=" O GLU c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 65 through 73 Processing helix chain 'd' and resid 3 through 15 Processing helix chain 'd' and resid 19 through 21 No H-bonds generated for 'chain 'd' and resid 19 through 21' Processing helix chain 'd' and resid 36 through 50 Processing helix chain 'd' and resid 56 through 61 removed outlier: 3.649A pdb=" N LYS d 61 " --> pdb=" O GLU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 73 Processing helix chain 'e' and resid 3 through 15 Processing helix chain 'e' and resid 19 through 21 No H-bonds generated for 'chain 'e' and resid 19 through 21' Processing helix chain 'e' and resid 36 through 50 Processing helix chain 'e' and resid 56 through 61 removed outlier: 3.650A pdb=" N LYS e 61 " --> pdb=" O GLU e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 65 through 73 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.522A pdb=" N GLN A 243 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 265 " --> pdb=" O MET A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.672A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS A 89 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 68 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS A 91 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR A 174 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS A 183 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= D, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.505A pdb=" N ILE A 431 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 455 through 462 removed outlier: 3.522A pdb=" N GLU A 455 " --> pdb=" O THR A 475 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= G, first strand: chain 'A' and resid 411 through 415 removed outlier: 6.624A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.522A pdb=" N GLN B 243 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE B 265 " --> pdb=" O MET B 219 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.672A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS B 89 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 68 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS B 91 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR B 174 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS B 183 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= K, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.505A pdb=" N ILE B 431 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 455 through 462 removed outlier: 3.522A pdb=" N GLU B 455 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= N, first strand: chain 'B' and resid 411 through 415 removed outlier: 6.624A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.522A pdb=" N GLN C 243 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 265 " --> pdb=" O MET C 219 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.673A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS C 89 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL C 68 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS C 91 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR C 174 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS C 183 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= R, first strand: chain 'C' and resid 431 through 433 removed outlier: 3.505A pdb=" N ILE C 431 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 455 through 462 removed outlier: 3.522A pdb=" N GLU C 455 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= U, first strand: chain 'C' and resid 411 through 415 removed outlier: 6.625A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.521A pdb=" N GLN D 243 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE D 265 " --> pdb=" O MET D 219 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.673A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS D 89 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 68 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS D 91 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR D 174 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS D 183 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= Y, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.505A pdb=" N ILE D 431 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 455 through 462 removed outlier: 3.522A pdb=" N GLU D 455 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= AB, first strand: chain 'D' and resid 411 through 415 removed outlier: 6.624A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.521A pdb=" N GLN E 243 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE E 265 " --> pdb=" O MET E 219 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.672A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS E 89 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL E 68 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS E 91 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR E 172 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E 185 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR E 174 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS E 183 " --> pdb=" O TYR E 174 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 361 through 363 Processing sheet with id= AF, first strand: chain 'E' and resid 431 through 433 removed outlier: 3.506A pdb=" N ILE E 431 " --> pdb=" O VAL E 438 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 455 through 462 removed outlier: 3.522A pdb=" N GLU E 455 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 317 through 319 Processing sheet with id= AI, first strand: chain 'E' and resid 411 through 415 removed outlier: 6.624A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.521A pdb=" N GLN F 243 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE F 265 " --> pdb=" O MET F 219 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.672A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS F 89 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL F 68 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS F 91 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR F 172 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL F 185 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR F 174 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS F 183 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 361 through 363 Processing sheet with id= AM, first strand: chain 'F' and resid 431 through 433 removed outlier: 3.505A pdb=" N ILE F 431 " --> pdb=" O VAL F 438 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 455 through 462 removed outlier: 3.522A pdb=" N GLU F 455 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 317 through 319 Processing sheet with id= AP, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.623A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2556 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: 10.60 Time building geometry restraints manager: 11.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5010 1.31 - 1.43: 7455 1.43 - 1.56: 17037 1.56 - 1.69: 12 1.69 - 1.82: 210 Bond restraints: 29724 Sorted by residual: bond pdb=" C5 AMP E 602 " pdb=" N7 AMP E 602 " ideal model delta sigma weight residual 1.350 1.537 -0.187 2.00e-02 2.50e+03 8.74e+01 bond pdb=" C5 AMP C 602 " pdb=" N7 AMP C 602 " ideal model delta sigma weight residual 1.350 1.537 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" C5 AMP F 602 " pdb=" N7 AMP F 602 " ideal model delta sigma weight residual 1.350 1.537 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" C5 AMP A 602 " pdb=" N7 AMP A 602 " ideal model delta sigma weight residual 1.350 1.537 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" C5 AMP B 602 " pdb=" N7 AMP B 602 " ideal model delta sigma weight residual 1.350 1.537 -0.187 2.00e-02 2.50e+03 8.73e+01 ... (remaining 29719 not shown) Histogram of bond angle deviations from ideal: 98.69 - 106.37: 840 106.37 - 114.05: 17263 114.05 - 121.73: 15471 121.73 - 129.41: 6481 129.41 - 137.08: 247 Bond angle restraints: 40302 Sorted by residual: angle pdb=" N GLU b 41 " pdb=" CA GLU b 41 " pdb=" C GLU b 41 " ideal model delta sigma weight residual 113.01 106.13 6.88 1.20e+00 6.94e-01 3.29e+01 angle pdb=" N GLU d 41 " pdb=" CA GLU d 41 " pdb=" C GLU d 41 " ideal model delta sigma weight residual 113.01 106.13 6.88 1.20e+00 6.94e-01 3.28e+01 angle pdb=" N GLU c 41 " pdb=" CA GLU c 41 " pdb=" C GLU c 41 " ideal model delta sigma weight residual 113.01 106.17 6.84 1.20e+00 6.94e-01 3.25e+01 angle pdb=" N GLU f 41 " pdb=" CA GLU f 41 " pdb=" C GLU f 41 " ideal model delta sigma weight residual 113.01 106.17 6.84 1.20e+00 6.94e-01 3.25e+01 angle pdb=" N GLU e 41 " pdb=" CA GLU e 41 " pdb=" C GLU e 41 " ideal model delta sigma weight residual 113.01 106.18 6.83 1.20e+00 6.94e-01 3.24e+01 ... (remaining 40297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 16289 21.46 - 42.93: 1194 42.93 - 64.39: 274 64.39 - 85.86: 63 85.86 - 107.32: 6 Dihedral angle restraints: 17826 sinusoidal: 7272 harmonic: 10554 Sorted by residual: dihedral pdb=" CA TYR E 33 " pdb=" C TYR E 33 " pdb=" N ALA E 34 " pdb=" CA ALA E 34 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR C 33 " pdb=" C TYR C 33 " pdb=" N ALA C 34 " pdb=" CA ALA C 34 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR A 33 " pdb=" C TYR A 33 " pdb=" N ALA A 34 " pdb=" CA ALA A 34 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 17823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4132 0.097 - 0.195: 392 0.195 - 0.292: 30 0.292 - 0.389: 6 0.389 - 0.487: 12 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CG LEU b 42 " pdb=" CB LEU b 42 " pdb=" CD1 LEU b 42 " pdb=" CD2 LEU b 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CG LEU f 42 " pdb=" CB LEU f 42 " pdb=" CD1 LEU f 42 " pdb=" CD2 LEU f 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CG LEU e 42 " pdb=" CB LEU e 42 " pdb=" CD1 LEU e 42 " pdb=" CD2 LEU e 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.92e+00 ... (remaining 4569 not shown) Planarity restraints: 5130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 370 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C LEU C 370 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU C 370 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO C 371 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 370 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C LEU F 370 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU F 370 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO F 371 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 370 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C LEU D 370 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU D 370 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO D 371 " 0.013 2.00e-02 2.50e+03 ... (remaining 5127 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 443 2.65 - 3.21: 26970 3.21 - 3.78: 44130 3.78 - 4.34: 66645 4.34 - 4.90: 105575 Nonbonded interactions: 243763 Sorted by model distance: nonbonded pdb=" OD1 ASP C 342 " pdb=" N GLN C 343 " model vdw 2.088 2.520 nonbonded pdb=" OD1 ASP B 342 " pdb=" N GLN B 343 " model vdw 2.088 2.520 nonbonded pdb=" OD1 ASP A 342 " pdb=" N GLN A 343 " model vdw 2.088 2.520 nonbonded pdb=" OD1 ASP E 342 " pdb=" N GLN E 343 " model vdw 2.088 2.520 nonbonded pdb=" OD1 ASP D 342 " pdb=" N GLN D 343 " model vdw 2.088 2.520 ... (remaining 243758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 2.120 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: 8.810 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 79.200 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.330 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:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.007 0.187 29724 Z= 0.433 Angle : 0.885 15.804 40302 Z= 0.453 Chirality : 0.060 0.487 4572 Planarity : 0.004 0.039 5130 Dihedral : 16.420 107.324 11022 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.76 % Allowed : 11.79 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3600 helix: 0.28 (0.14), residues: 1350 sheet: -0.90 (0.19), residues: 648 loop : -1.31 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 290 HIS 0.005 0.001 HIS D 228 PHE 0.013 0.001 PHE D 315 TYR 0.013 0.002 TYR D 245 ARG 0.003 0.001 ARG F 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 219 MET cc_start: 0.9410 (ttp) cc_final: 0.9140 (ttm) REVERT: D 150 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7780 (mtm-85) REVERT: D 160 ASN cc_start: 0.8368 (m110) cc_final: 0.8163 (m-40) REVERT: E 160 ASN cc_start: 0.8399 (m110) cc_final: 0.8198 (m-40) REVERT: F 219 MET cc_start: 0.9407 (ttp) cc_final: 0.9122 (ttm) outliers start: 24 outliers final: 13 residues processed: 281 average time/residue: 1.6543 time to fit residues: 533.8887 Evaluate side-chains 215 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain f residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 260 GLN A 343 GLN B 126 GLN B 343 GLN C 343 GLN D 343 GLN E 343 GLN F 343 GLN ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 66 GLN f 75 HIS a 66 GLN a 75 HIS b 66 GLN b 75 HIS c 66 GLN c 75 HIS d 66 GLN d 75 HIS e 66 GLN e 75 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29724 Z= 0.346 Angle : 0.683 9.603 40302 Z= 0.349 Chirality : 0.051 0.214 4572 Planarity : 0.004 0.040 5130 Dihedral : 8.792 85.107 4034 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.07 % Allowed : 12.58 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3600 helix: 0.33 (0.14), residues: 1374 sheet: -0.74 (0.19), residues: 660 loop : -1.39 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 290 HIS 0.006 0.001 HIS D 267 PHE 0.028 0.002 PHE f 50 TYR 0.015 0.002 TYR D 245 ARG 0.003 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 206 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: B 85 MET cc_start: 0.9335 (mtm) cc_final: 0.9044 (mtp) REVERT: C 163 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (p0) REVERT: C 259 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: C 342 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: D 160 ASN cc_start: 0.8389 (m110) cc_final: 0.8079 (m-40) REVERT: D 292 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8766 (p) REVERT: D 337 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8365 (mt) REVERT: E 160 ASN cc_start: 0.8417 (m110) cc_final: 0.8206 (m-40) REVERT: E 337 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8397 (mt) REVERT: F 163 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7899 (p0) REVERT: F 342 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: F 484 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5613 (mm-30) outliers start: 97 outliers final: 28 residues processed: 282 average time/residue: 1.5904 time to fit residues: 519.1158 Evaluate side-chains 241 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain e residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 267 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 347 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN D 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29724 Z= 0.343 Angle : 0.657 9.345 40302 Z= 0.337 Chirality : 0.050 0.211 4572 Planarity : 0.004 0.043 5130 Dihedral : 8.553 77.651 4032 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.58 % Allowed : 13.59 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3600 helix: 0.18 (0.14), residues: 1440 sheet: -0.75 (0.19), residues: 660 loop : -1.38 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 290 HIS 0.005 0.001 HIS F 213 PHE 0.015 0.002 PHE B 315 TYR 0.016 0.002 TYR D 245 ARG 0.004 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 198 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.9333 (mtm) cc_final: 0.9106 (mtp) REVERT: B 337 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8606 (mm) REVERT: C 92 MET cc_start: 0.9190 (mtm) cc_final: 0.8938 (mpp) REVERT: C 163 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (p0) REVERT: C 232 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8794 (mm) REVERT: C 259 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: C 337 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8469 (mm) REVERT: C 342 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: D 150 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7720 (mtm-85) REVERT: D 160 ASN cc_start: 0.8373 (m110) cc_final: 0.8140 (m-40) REVERT: D 337 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8380 (mt) REVERT: E 160 ASN cc_start: 0.8407 (m110) cc_final: 0.8161 (m-40) REVERT: E 337 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8366 (mt) REVERT: F 163 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7889 (p0) REVERT: F 232 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8809 (mm) REVERT: F 342 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: F 484 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5565 (mm-30) outliers start: 113 outliers final: 39 residues processed: 296 average time/residue: 1.5429 time to fit residues: 531.2183 Evaluate side-chains 243 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain a residue 13 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 20.0000 chunk 242 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 153 optimal weight: 20.0000 chunk 216 optimal weight: 0.0070 chunk 323 optimal weight: 6.9990 chunk 342 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 306 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 ASN E 206 ASN E 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29724 Z= 0.292 Angle : 0.623 7.729 40302 Z= 0.319 Chirality : 0.048 0.204 4572 Planarity : 0.004 0.043 5130 Dihedral : 8.431 73.768 4032 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.30 % Allowed : 14.54 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.82 (0.13), residues: 3600 helix: 0.46 (0.14), residues: 1392 sheet: -0.74 (0.19), residues: 660 loop : -1.33 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 466 HIS 0.005 0.001 HIS F 213 PHE 0.014 0.002 PHE B 315 TYR 0.013 0.002 TYR A 148 ARG 0.003 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 195 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8544 (mp) REVERT: A 134 VAL cc_start: 0.9049 (t) cc_final: 0.8813 (t) REVERT: A 309 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: B 18 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 134 VAL cc_start: 0.9081 (t) cc_final: 0.8869 (t) REVERT: B 429 ASP cc_start: 0.5255 (OUTLIER) cc_final: 0.4274 (m-30) REVERT: C 92 MET cc_start: 0.9124 (mtm) cc_final: 0.8860 (mpp) REVERT: C 163 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7853 (p0) REVERT: C 232 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8777 (mm) REVERT: C 259 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: C 337 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8411 (mm) REVERT: C 342 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: D 160 ASN cc_start: 0.8408 (m110) cc_final: 0.8166 (m-40) REVERT: D 337 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8336 (mt) REVERT: D 429 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.4564 (m-30) REVERT: E 158 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: E 160 ASN cc_start: 0.8424 (m110) cc_final: 0.8175 (m-40) REVERT: E 337 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8333 (mt) REVERT: F 163 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7841 (p0) REVERT: F 232 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8846 (mm) REVERT: F 309 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: F 342 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: b 44 MET cc_start: 0.4463 (OUTLIER) cc_final: 0.4104 (mpt) REVERT: e 30 GLU cc_start: 0.3675 (OUTLIER) cc_final: 0.2778 (mm-30) outliers start: 104 outliers final: 44 residues processed: 283 average time/residue: 1.4595 time to fit residues: 482.3370 Evaluate side-chains 263 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 200 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 174 optimal weight: 0.0770 chunk 307 optimal weight: 0.0020 chunk 86 optimal weight: 0.9980 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN C 126 GLN E 260 GLN F 17 ASN F 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29724 Z= 0.149 Angle : 0.549 7.500 40302 Z= 0.276 Chirality : 0.045 0.207 4572 Planarity : 0.003 0.039 5130 Dihedral : 7.845 63.676 4032 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.98 % Allowed : 15.37 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.45 (0.14), residues: 3600 helix: 0.82 (0.14), residues: 1386 sheet: -0.60 (0.20), residues: 660 loop : -1.14 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 290 HIS 0.004 0.001 HIS E 414 PHE 0.009 0.001 PHE E 225 TYR 0.012 0.001 TYR C 148 ARG 0.002 0.000 ARG F 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 239 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8533 (mp) REVERT: A 206 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8536 (m-40) REVERT: B 18 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8472 (mp) REVERT: C 259 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: C 337 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8387 (mm) REVERT: C 342 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: C 429 ASP cc_start: 0.5710 (OUTLIER) cc_final: 0.5122 (m-30) REVERT: D 150 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7730 (mtm-85) REVERT: D 160 ASN cc_start: 0.8348 (m110) cc_final: 0.8063 (m-40) REVERT: D 429 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.4728 (m-30) REVERT: E 160 ASN cc_start: 0.8403 (m110) cc_final: 0.8130 (m-40) REVERT: E 285 MET cc_start: 0.7986 (mtp) cc_final: 0.7747 (mtp) REVERT: E 484 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5551 (mm-30) REVERT: F 163 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7796 (p0) REVERT: F 309 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: F 342 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: e 30 GLU cc_start: 0.3490 (OUTLIER) cc_final: 0.2569 (mm-30) outliers start: 94 outliers final: 24 residues processed: 318 average time/residue: 1.4699 time to fit residues: 546.6333 Evaluate side-chains 249 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 342 optimal weight: 40.0000 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 28 optimal weight: 0.0370 chunk 113 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29724 Z= 0.161 Angle : 0.556 8.753 40302 Z= 0.278 Chirality : 0.045 0.198 4572 Planarity : 0.003 0.037 5130 Dihedral : 7.328 59.403 4026 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.69 % Allowed : 16.29 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.44 (0.14), residues: 3600 helix: 0.76 (0.14), residues: 1434 sheet: -0.54 (0.20), residues: 660 loop : -1.15 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 466 HIS 0.003 0.001 HIS F 414 PHE 0.012 0.001 PHE B 315 TYR 0.012 0.001 TYR C 148 ARG 0.001 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 238 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8433 (mp) REVERT: C 259 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: C 337 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8354 (mm) REVERT: C 429 ASP cc_start: 0.5466 (OUTLIER) cc_final: 0.4710 (m-30) REVERT: D 150 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7660 (mtm-85) REVERT: D 160 ASN cc_start: 0.8346 (m110) cc_final: 0.8057 (m-40) REVERT: D 429 ASP cc_start: 0.5745 (OUTLIER) cc_final: 0.4523 (m-30) REVERT: E 160 ASN cc_start: 0.8417 (m110) cc_final: 0.8172 (m-40) REVERT: E 484 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5440 (mm-30) REVERT: F 163 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7787 (p0) REVERT: F 309 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: e 30 GLU cc_start: 0.3436 (OUTLIER) cc_final: 0.2523 (mm-30) outliers start: 85 outliers final: 32 residues processed: 309 average time/residue: 1.5862 time to fit residues: 579.6824 Evaluate side-chains 273 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain d residue 72 ILE Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 288 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 341 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 343 GLN F 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29724 Z= 0.239 Angle : 0.596 8.419 40302 Z= 0.301 Chirality : 0.047 0.201 4572 Planarity : 0.004 0.039 5130 Dihedral : 7.430 61.314 4024 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.50 % Allowed : 16.57 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3600 helix: 0.67 (0.14), residues: 1440 sheet: -0.58 (0.20), residues: 660 loop : -1.21 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 290 HIS 0.004 0.001 HIS C 228 PHE 0.016 0.001 PHE B 315 TYR 0.012 0.001 TYR E 245 ARG 0.001 0.000 ARG E 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 226 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.4925 (OUTLIER) cc_final: 0.4385 (pt) REVERT: B 18 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8479 (mp) REVERT: B 506 LEU cc_start: 0.4864 (OUTLIER) cc_final: 0.4331 (pt) REVERT: C 259 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: C 337 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8347 (mm) REVERT: C 429 ASP cc_start: 0.5517 (OUTLIER) cc_final: 0.4652 (m-30) REVERT: D 160 ASN cc_start: 0.8394 (m110) cc_final: 0.8096 (m-40) REVERT: D 337 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8291 (mt) REVERT: D 429 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.4500 (m-30) REVERT: E 160 ASN cc_start: 0.8442 (m110) cc_final: 0.8188 (m-40) REVERT: E 337 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8314 (mt) REVERT: E 484 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5485 (mm-30) REVERT: F 163 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7809 (p0) REVERT: F 309 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: e 30 GLU cc_start: 0.3531 (OUTLIER) cc_final: 0.2602 (mm-30) outliers start: 79 outliers final: 36 residues processed: 294 average time/residue: 1.5426 time to fit residues: 526.1217 Evaluate side-chains 272 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 223 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain d residue 72 ILE Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 203 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29724 Z= 0.195 Angle : 0.577 9.836 40302 Z= 0.291 Chirality : 0.046 0.197 4572 Planarity : 0.004 0.038 5130 Dihedral : 7.283 59.760 4024 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.28 % Allowed : 17.14 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.52 (0.14), residues: 3600 helix: 0.71 (0.14), residues: 1434 sheet: -0.51 (0.21), residues: 594 loop : -1.23 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 466 HIS 0.004 0.001 HIS E 39 PHE 0.013 0.001 PHE A 315 TYR 0.012 0.001 TYR F 148 ARG 0.002 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 229 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.4984 (OUTLIER) cc_final: 0.4415 (pt) REVERT: B 18 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8473 (mp) REVERT: C 259 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: C 337 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (mm) REVERT: C 429 ASP cc_start: 0.5530 (OUTLIER) cc_final: 0.4777 (m-30) REVERT: D 160 ASN cc_start: 0.8386 (m110) cc_final: 0.8142 (m-40) REVERT: D 337 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8265 (mt) REVERT: D 429 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.4598 (m-30) REVERT: E 160 ASN cc_start: 0.8446 (m110) cc_final: 0.8193 (m-40) REVERT: F 163 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7823 (p0) REVERT: F 309 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: F 342 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: f 49 GLU cc_start: 0.1393 (OUTLIER) cc_final: 0.1185 (tt0) REVERT: e 30 GLU cc_start: 0.3521 (OUTLIER) cc_final: 0.2575 (mm-30) outliers start: 72 outliers final: 40 residues processed: 291 average time/residue: 1.5071 time to fit residues: 510.2804 Evaluate side-chains 268 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 216 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 49 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 chunk 298 optimal weight: 0.9980 chunk 317 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 287 optimal weight: 0.7980 chunk 300 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 532 HIS E 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 29724 Z= 0.376 Angle : 0.672 9.659 40302 Z= 0.344 Chirality : 0.051 0.226 4572 Planarity : 0.004 0.047 5130 Dihedral : 7.737 65.760 4024 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.44 % Allowed : 16.92 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.14), residues: 3600 helix: 0.52 (0.14), residues: 1434 sheet: -0.60 (0.20), residues: 648 loop : -1.33 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 290 HIS 0.005 0.001 HIS F 213 PHE 0.019 0.002 PHE B 315 TYR 0.014 0.002 TYR E 245 ARG 0.003 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 197 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4279 (pt) REVERT: B 18 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 506 LEU cc_start: 0.4741 (OUTLIER) cc_final: 0.4168 (pt) REVERT: C 259 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: C 337 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8362 (mm) REVERT: C 429 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.4649 (m-30) REVERT: D 18 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8549 (mp) REVERT: D 160 ASN cc_start: 0.8449 (m110) cc_final: 0.8199 (m-40) REVERT: D 337 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8372 (mt) REVERT: D 429 ASP cc_start: 0.5708 (OUTLIER) cc_final: 0.4607 (m-30) REVERT: E 18 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8506 (mp) REVERT: E 337 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8294 (mt) REVERT: F 163 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7816 (p0) REVERT: F 309 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: F 342 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: f 49 GLU cc_start: 0.1789 (OUTLIER) cc_final: 0.1483 (tt0) REVERT: e 30 GLU cc_start: 0.3731 (OUTLIER) cc_final: 0.2786 (mm-30) outliers start: 77 outliers final: 39 residues processed: 265 average time/residue: 1.5045 time to fit residues: 463.9562 Evaluate side-chains 250 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 49 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 324 optimal weight: 40.0000 chunk 280 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 172 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29724 Z= 0.249 Angle : 0.616 11.494 40302 Z= 0.312 Chirality : 0.048 0.195 4572 Planarity : 0.004 0.044 5130 Dihedral : 7.544 63.364 4024 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.96 % Allowed : 17.33 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.69 (0.14), residues: 3600 helix: 0.56 (0.14), residues: 1434 sheet: -0.66 (0.20), residues: 660 loop : -1.29 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 466 HIS 0.004 0.001 HIS D 39 PHE 0.014 0.001 PHE B 315 TYR 0.014 0.001 TYR A 148 ARG 0.002 0.000 ARG E 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.4336 (pt) REVERT: B 18 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 506 LEU cc_start: 0.4812 (OUTLIER) cc_final: 0.4236 (pt) REVERT: C 259 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: C 337 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8341 (mm) REVERT: C 429 ASP cc_start: 0.5457 (OUTLIER) cc_final: 0.4589 (m-30) REVERT: D 18 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8538 (mp) REVERT: D 160 ASN cc_start: 0.8440 (m110) cc_final: 0.8194 (m-40) REVERT: D 337 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8308 (mt) REVERT: D 429 ASP cc_start: 0.5549 (OUTLIER) cc_final: 0.4513 (m-30) REVERT: E 18 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8489 (mp) REVERT: E 160 ASN cc_start: 0.8454 (m110) cc_final: 0.8200 (m-40) REVERT: E 337 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8293 (mm) REVERT: E 484 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5531 (mm-30) REVERT: F 163 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7845 (p0) REVERT: F 309 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: F 342 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: f 49 GLU cc_start: 0.1601 (OUTLIER) cc_final: 0.1321 (tt0) REVERT: e 30 GLU cc_start: 0.3711 (OUTLIER) cc_final: 0.2742 (mm-30) outliers start: 62 outliers final: 37 residues processed: 261 average time/residue: 1.5783 time to fit residues: 479.8071 Evaluate side-chains 249 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 195 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain f residue 49 GLU Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain e residue 30 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 0.2980 chunk 299 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117332 restraints weight = 32285.276| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.10 r_work: 0.3141 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29724 Z= 0.245 Angle : 0.614 10.625 40302 Z= 0.311 Chirality : 0.048 0.198 4572 Planarity : 0.004 0.044 5130 Dihedral : 7.495 63.710 4024 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.15 % Allowed : 17.08 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3600 helix: 0.59 (0.14), residues: 1434 sheet: -0.66 (0.20), residues: 660 loop : -1.29 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 466 HIS 0.004 0.001 HIS E 39 PHE 0.014 0.001 PHE B 315 TYR 0.013 0.001 TYR A 148 ARG 0.002 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9415.03 seconds wall clock time: 170 minutes 5.68 seconds (10205.68 seconds total)