Starting phenix.real_space_refine on Fri Feb 16 19:14:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/02_2024/7tz5_26202_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/02_2024/7tz5_26202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/02_2024/7tz5_26202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/02_2024/7tz5_26202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/02_2024/7tz5_26202_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/02_2024/7tz5_26202_neut.pdb" } resolution = 3.41 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10056 2.51 5 N 2775 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 98": "OD1" <-> "OD2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 108": "OD1" <-> "OD2" Residue "N TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 108": "OD1" <-> "OD2" Residue "A ASP 32": "OD1" <-> "OD2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 175": "OD1" <-> "OD2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 32": "OD1" <-> "OD2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16023 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 893 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "I" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 893 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "J" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 893 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 763 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 763 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 763 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3685 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3685 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3685 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 8.76, per 1000 atoms: 0.55 Number of scatterers: 16023 At special positions: 0 Unit cell: (119.402, 112.564, 179.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3120 8.00 N 2775 7.00 C 10056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.04 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.04 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.9 seconds 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 51 sheets defined 17.2% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 404 through 455 WARNING: missing atoms! Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.543A pdb=" N ASN A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 4.144A pdb=" N LEU A 496 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 385 Processing helix chain 'B' and resid 404 through 455 WARNING: missing atoms! Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.536A pdb=" N ASN B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.127A pdb=" N LEU B 496 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 385 Processing helix chain 'C' and resid 404 through 455 WARNING: missing atoms! Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.539A pdb=" N ASN C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 496 removed outlier: 4.132A pdb=" N LEU C 496 " --> pdb=" O ASP C 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.604A pdb=" N GLN H 3 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 5 " --> pdb=" O LYS H 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.556A pdb=" N VAL H 21 " --> pdb=" O MET H 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 50 through 52 removed outlier: 3.568A pdb=" N ARG H 43 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY H 108 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE H 115 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 50 through 52 removed outlier: 3.568A pdb=" N ARG H 43 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 100 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.602A pdb=" N GLN I 3 " --> pdb=" O SER I 26 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL I 5 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AA7, first strand: chain 'I' and resid 50 through 52 removed outlier: 3.530A pdb=" N ARG I 43 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY I 108 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE I 115 " --> pdb=" O GLY I 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 50 through 52 removed outlier: 3.530A pdb=" N ARG I 43 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I 100 " --> pdb=" O VAL I 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.607A pdb=" N GLN J 3 " --> pdb=" O SER J 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 5 " --> pdb=" O LYS J 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 20 through 21 removed outlier: 3.529A pdb=" N VAL J 21 " --> pdb=" O MET J 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 50 through 52 removed outlier: 3.550A pdb=" N ARG J 43 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY J 108 " --> pdb=" O PHE J 115 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE J 115 " --> pdb=" O GLY J 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 50 through 52 removed outlier: 3.550A pdb=" N ARG J 43 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA J 100 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL J 124 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 25 Processing sheet with id=AB5, first strand: chain 'L' and resid 51 through 55 removed outlier: 6.483A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 20 through 25 Processing sheet with id=AB7, first strand: chain 'M' and resid 51 through 55 removed outlier: 6.502A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 20 through 25 Processing sheet with id=AB9, first strand: chain 'N' and resid 51 through 55 removed outlier: 6.498A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.890A pdb=" N GLY A 362 " --> pdb=" O HIS A 355 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 355 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 11 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 469 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AC3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.210A pdb=" N CYS A 277 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AC7, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.980A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.881A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AD1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.489A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 360 through 363 removed outlier: 3.907A pdb=" N GLY B 362 " --> pdb=" O HIS B 355 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS B 355 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 11 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 469 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AD5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.090A pdb=" N ILE B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 53 " --> pdb=" O CYS B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 58 through 61 Processing sheet with id=AD9, first strand: chain 'B' and resid 100 through 101 removed outlier: 4.985A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.882A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.556A pdb=" N SER B 146 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AE4, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.508A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 360 through 363 removed outlier: 3.904A pdb=" N GLY C 362 " --> pdb=" O HIS C 355 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS C 355 " --> pdb=" O GLY C 362 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 11 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 469 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AE7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AE8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AE9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.128A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.893A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 100 through 101 removed outlier: 4.977A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.881A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.583A pdb=" N SER C 146 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AF6, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.501A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1623 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: 5.54 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5434 1.36 - 1.50: 4784 1.50 - 1.63: 6069 1.63 - 1.77: 36 1.77 - 1.91: 66 Bond restraints: 16389 Sorted by residual: bond pdb=" CB CYS A 305 " pdb=" SG CYS A 305 " ideal model delta sigma weight residual 1.808 1.664 0.144 3.30e-02 9.18e+02 1.91e+01 bond pdb=" CB CYS B 305 " pdb=" SG CYS B 305 " ideal model delta sigma weight residual 1.808 1.665 0.143 3.30e-02 9.18e+02 1.89e+01 bond pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " ideal model delta sigma weight residual 1.808 1.671 0.137 3.30e-02 9.18e+02 1.71e+01 bond pdb=" CB CYS C 305 " pdb=" SG CYS C 305 " ideal model delta sigma weight residual 1.808 1.672 0.136 3.30e-02 9.18e+02 1.70e+01 bond pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " ideal model delta sigma weight residual 1.808 1.913 -0.105 3.30e-02 9.18e+02 1.01e+01 ... (remaining 16384 not shown) Histogram of bond angle deviations from ideal: 92.98 - 103.40: 210 103.40 - 113.81: 9258 113.81 - 124.23: 12399 124.23 - 134.65: 436 134.65 - 145.06: 5 Bond angle restraints: 22308 Sorted by residual: angle pdb=" CA CYS A 305 " pdb=" CB CYS A 305 " pdb=" SG CYS A 305 " ideal model delta sigma weight residual 114.40 145.06 -30.66 2.30e+00 1.89e-01 1.78e+02 angle pdb=" CA CYS C 305 " pdb=" CB CYS C 305 " pdb=" SG CYS C 305 " ideal model delta sigma weight residual 114.40 144.33 -29.93 2.30e+00 1.89e-01 1.69e+02 angle pdb=" CA CYS B 305 " pdb=" CB CYS B 305 " pdb=" SG CYS B 305 " ideal model delta sigma weight residual 114.40 143.99 -29.59 2.30e+00 1.89e-01 1.66e+02 angle pdb=" CA CYS A 277 " pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " ideal model delta sigma weight residual 114.40 139.92 -25.52 2.30e+00 1.89e-01 1.23e+02 angle pdb=" C CYS A 52 " pdb=" CA CYS A 52 " pdb=" CB CYS A 52 " ideal model delta sigma weight residual 109.65 126.76 -17.11 1.71e+00 3.42e-01 1.00e+02 ... (remaining 22303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8903 17.94 - 35.87: 590 35.87 - 53.81: 110 53.81 - 71.74: 41 71.74 - 89.68: 9 Dihedral angle restraints: 9653 sinusoidal: 3548 harmonic: 6105 Sorted by residual: dihedral pdb=" CB CYS B 52 " pdb=" SG CYS B 52 " pdb=" SG CYS B 277 " pdb=" CB CYS B 277 " ideal model delta sinusoidal sigma weight residual -86.00 -16.69 -69.31 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -16.89 -69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS B 473 " pdb=" SG CYS B 473 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual 93.00 25.42 67.58 1 1.00e+01 1.00e-02 5.94e+01 ... (remaining 9650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2338 0.125 - 0.249: 113 0.249 - 0.374: 5 0.374 - 0.498: 0 0.498 - 0.623: 4 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA CYS B 305 " pdb=" N CYS B 305 " pdb=" C CYS B 305 " pdb=" CB CYS B 305 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.70e+00 chirality pdb=" CA CYS A 305 " pdb=" N CYS A 305 " pdb=" C CYS A 305 " pdb=" CB CYS A 305 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" CA CYS C 305 " pdb=" N CYS C 305 " pdb=" C CYS C 305 " pdb=" CB CYS C 305 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.29e+00 ... (remaining 2457 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 471 " -0.015 2.00e-02 2.50e+03 1.54e-02 3.56e+00 pdb=" CG HIS C 471 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS C 471 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS C 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS C 471 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 471 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 471 " -0.015 2.00e-02 2.50e+03 1.54e-02 3.55e+00 pdb=" CG HIS A 471 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 471 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 471 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 471 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 471 " -0.015 2.00e-02 2.50e+03 1.51e-02 3.42e+00 pdb=" CG HIS B 471 " 0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS B 471 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 471 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 471 " -0.007 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 292 2.63 - 3.20: 14461 3.20 - 3.77: 23490 3.77 - 4.33: 32492 4.33 - 4.90: 54975 Nonbonded interactions: 125710 Sorted by model distance: nonbonded pdb=" NH1 ARG A 492 " pdb=" O ARG B 499 " model vdw 2.067 2.520 nonbonded pdb=" O ARG A 499 " pdb=" NH1 ARG C 492 " model vdw 2.081 2.520 nonbonded pdb=" NH1 ARG B 492 " pdb=" O ARG C 499 " model vdw 2.085 2.520 nonbonded pdb=" OG1 THR N 5 " pdb=" O GLY N 25 " model vdw 2.147 2.440 nonbonded pdb=" NE2 GLN N 17 " pdb=" O LEU N 94 " model vdw 2.152 2.520 ... (remaining 125705 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 6.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 28.050 Check model and map are aligned: 0.400 Set scattering table: 0.150 Process input model: 42.930 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.009 0.144 16389 Z= 0.600 Angle : 1.180 30.662 22308 Z= 0.664 Chirality : 0.066 0.623 2460 Planarity : 0.005 0.032 2922 Dihedral : 13.200 89.677 5723 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.62 % Favored : 88.95 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % Favored : 99.09 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 3.12 % 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: -2.38 (0.16), residues: 2118 helix: 0.83 (0.25), residues: 324 sheet: -1.58 (0.22), residues: 489 loop : -2.33 (0.14), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 180 HIS 0.015 0.003 HIS A 471 PHE 0.026 0.003 PHE C 159 TYR 0.021 0.002 TYR L 55 ARG 0.014 0.001 ARG N 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 225 time to evaluate : 1.851 Fit side-chains REVERT: H 52 TRP cc_start: 0.8600 (t-100) cc_final: 0.8335 (t60) REVERT: L 103 TYR cc_start: 0.8448 (m-80) cc_final: 0.7725 (m-10) REVERT: M 103 TYR cc_start: 0.8416 (m-10) cc_final: 0.8010 (m-10) REVERT: A 307 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7550 (mmm-85) REVERT: B 307 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7594 (mmm-85) outliers start: 5 outliers final: 5 residues processed: 230 average time/residue: 0.2825 time to fit residues: 96.7305 Evaluate side-chains 190 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 122 optimal weight: 0.3980 chunk 190 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16389 Z= 0.205 Angle : 0.637 6.389 22308 Z= 0.342 Chirality : 0.047 0.186 2460 Planarity : 0.004 0.037 2922 Dihedral : 6.001 59.360 2315 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.40 % Allowed : 6.63 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.59 (0.17), residues: 2118 helix: 2.51 (0.26), residues: 324 sheet: -1.04 (0.22), residues: 495 loop : -2.13 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 421 HIS 0.005 0.001 HIS H 112 PHE 0.018 0.001 PHE B 193 TYR 0.019 0.001 TYR A 423 ARG 0.006 0.001 ARG C 383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 TYR cc_start: 0.8308 (m-80) cc_final: 0.7624 (m-10) REVERT: M 103 TYR cc_start: 0.8293 (m-10) cc_final: 0.7811 (m-10) REVERT: A 38 ASN cc_start: 0.6802 (t0) cc_final: 0.6354 (p0) REVERT: C 38 ASN cc_start: 0.6824 (t0) cc_final: 0.6497 (p0) outliers start: 23 outliers final: 14 residues processed: 231 average time/residue: 0.2939 time to fit residues: 99.0904 Evaluate side-chains 209 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16389 Z= 0.287 Angle : 0.607 5.856 22308 Z= 0.324 Chirality : 0.046 0.161 2460 Planarity : 0.004 0.036 2922 Dihedral : 5.765 56.441 2315 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.62 % Allowed : 8.95 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.43 (0.17), residues: 2118 helix: 2.94 (0.27), residues: 321 sheet: -1.01 (0.22), residues: 510 loop : -2.07 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 52 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.002 PHE C 159 TYR 0.011 0.001 TYR B 423 ARG 0.005 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 103 TYR cc_start: 0.8296 (m-10) cc_final: 0.7787 (m-10) REVERT: A 223 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8750 (p) REVERT: C 38 ASN cc_start: 0.6858 (t0) cc_final: 0.6453 (p0) outliers start: 43 outliers final: 21 residues processed: 231 average time/residue: 0.2875 time to fit residues: 98.0994 Evaluate side-chains 212 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 HIS I 44 GLN J 112 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16389 Z= 0.400 Angle : 0.646 7.735 22308 Z= 0.343 Chirality : 0.047 0.165 2460 Planarity : 0.005 0.040 2922 Dihedral : 5.856 56.450 2315 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.53 % Allowed : 10.96 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.60 (0.17), residues: 2118 helix: 2.87 (0.28), residues: 324 sheet: -1.19 (0.22), residues: 501 loop : -2.18 (0.15), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 52 HIS 0.006 0.002 HIS C 183 PHE 0.014 0.002 PHE A 159 TYR 0.012 0.002 TYR H 102 ARG 0.004 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 193 time to evaluate : 1.806 Fit side-chains REVERT: L 91 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7367 (tt) REVERT: L 98 ASP cc_start: 0.6780 (m-30) cc_final: 0.6565 (m-30) REVERT: M 91 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7289 (tt) REVERT: M 103 TYR cc_start: 0.8316 (m-10) cc_final: 0.7783 (m-10) REVERT: N 91 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7328 (tt) REVERT: A 223 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 307 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7629 (mmm-85) REVERT: B 307 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7610 (mmm-85) outliers start: 58 outliers final: 32 residues processed: 237 average time/residue: 0.2786 time to fit residues: 97.6537 Evaluate side-chains 217 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 173 optimal weight: 0.0040 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 182 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16389 Z= 0.169 Angle : 0.546 6.476 22308 Z= 0.288 Chirality : 0.044 0.143 2460 Planarity : 0.004 0.042 2922 Dihedral : 5.314 55.079 2315 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.43 % Allowed : 13.09 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.35 (0.18), residues: 2118 helix: 3.07 (0.27), residues: 324 sheet: -1.00 (0.22), residues: 501 loop : -2.02 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS I 112 PHE 0.011 0.001 PHE C 448 TYR 0.007 0.001 TYR H 37 ARG 0.006 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: H 50 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8572 (mp) REVERT: H 52 TRP cc_start: 0.8487 (t-100) cc_final: 0.8212 (t60) REVERT: L 91 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7286 (tt) REVERT: M 91 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7125 (tt) REVERT: M 103 TYR cc_start: 0.8193 (m-10) cc_final: 0.7654 (m-10) REVERT: N 91 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7265 (tt) REVERT: A 223 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8715 (p) REVERT: B 223 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8735 (p) REVERT: B 423 TYR cc_start: 0.8421 (t80) cc_final: 0.8149 (t80) outliers start: 40 outliers final: 18 residues processed: 235 average time/residue: 0.3136 time to fit residues: 108.8664 Evaluate side-chains 209 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16389 Z= 0.276 Angle : 0.579 7.729 22308 Z= 0.302 Chirality : 0.045 0.161 2460 Planarity : 0.004 0.041 2922 Dihedral : 5.257 53.194 2315 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.04 % Allowed : 13.45 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.42 (0.18), residues: 2118 helix: 3.10 (0.28), residues: 324 sheet: -1.06 (0.22), residues: 498 loop : -2.09 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.004 0.001 HIS A 183 PHE 0.013 0.002 PHE C 448 TYR 0.008 0.001 TYR H 102 ARG 0.005 0.000 ARG N 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 186 time to evaluate : 1.923 Fit side-chains REVERT: H 50 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8589 (mp) REVERT: L 91 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7315 (tt) REVERT: M 91 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7122 (tt) REVERT: M 103 TYR cc_start: 0.8225 (m-10) cc_final: 0.7668 (m-10) REVERT: N 91 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7240 (tt) REVERT: A 223 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8702 (p) outliers start: 50 outliers final: 30 residues processed: 223 average time/residue: 0.2861 time to fit residues: 94.1265 Evaluate side-chains 216 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 20.0000 chunk 22 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16389 Z= 0.187 Angle : 0.536 5.617 22308 Z= 0.281 Chirality : 0.044 0.147 2460 Planarity : 0.004 0.046 2922 Dihedral : 4.928 51.349 2315 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.98 % Allowed : 13.09 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.35 (0.18), residues: 2118 helix: 3.16 (0.27), residues: 324 sheet: -1.05 (0.22), residues: 504 loop : -2.04 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.004 0.001 HIS I 112 PHE 0.011 0.001 PHE C 448 TYR 0.009 0.001 TYR N 103 ARG 0.006 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 2.030 Fit side-chains REVERT: H 50 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8553 (mp) REVERT: H 52 TRP cc_start: 0.8449 (t-100) cc_final: 0.8171 (t60) REVERT: L 91 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7281 (tt) REVERT: M 91 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7057 (tt) REVERT: M 103 TYR cc_start: 0.8181 (m-10) cc_final: 0.7617 (m-10) REVERT: N 91 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7233 (tt) REVERT: A 175 ASP cc_start: 0.7493 (m-30) cc_final: 0.7286 (m-30) REVERT: A 223 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (p) REVERT: B 223 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8654 (p) outliers start: 49 outliers final: 24 residues processed: 235 average time/residue: 0.2680 time to fit residues: 94.2261 Evaluate side-chains 215 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 184 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16389 Z= 0.300 Angle : 0.582 6.160 22308 Z= 0.305 Chirality : 0.045 0.151 2460 Planarity : 0.004 0.050 2922 Dihedral : 5.038 49.882 2314 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.80 % Allowed : 13.39 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.46 (0.18), residues: 2118 helix: 3.14 (0.28), residues: 324 sheet: -1.18 (0.22), residues: 504 loop : -2.11 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 52 HIS 0.004 0.001 HIS C 183 PHE 0.012 0.002 PHE C 159 TYR 0.015 0.001 TYR J 88 ARG 0.008 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.796 Fit side-chains REVERT: H 50 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8592 (mp) REVERT: L 91 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7261 (tt) REVERT: M 91 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7063 (tt) REVERT: M 103 TYR cc_start: 0.8226 (m-10) cc_final: 0.7650 (m-10) REVERT: N 91 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7244 (tt) REVERT: N 103 TYR cc_start: 0.8179 (m-10) cc_final: 0.7925 (m-10) REVERT: A 223 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 390 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7177 (mp0) outliers start: 46 outliers final: 33 residues processed: 223 average time/residue: 0.2995 time to fit residues: 99.7922 Evaluate side-chains 223 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16389 Z= 0.221 Angle : 0.559 6.726 22308 Z= 0.292 Chirality : 0.044 0.144 2460 Planarity : 0.004 0.050 2922 Dihedral : 4.897 48.127 2314 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.74 % Allowed : 13.63 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.44 (0.18), residues: 2118 helix: 3.08 (0.27), residues: 324 sheet: -1.15 (0.22), residues: 504 loop : -2.07 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 52 HIS 0.004 0.001 HIS I 112 PHE 0.012 0.001 PHE A 448 TYR 0.015 0.001 TYR J 88 ARG 0.008 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 1.899 Fit side-chains REVERT: H 50 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8573 (mp) REVERT: H 52 TRP cc_start: 0.8479 (t-100) cc_final: 0.8194 (t60) REVERT: L 91 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7203 (tt) REVERT: M 91 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7014 (tt) REVERT: M 103 TYR cc_start: 0.8192 (m-10) cc_final: 0.7612 (m-10) REVERT: N 91 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7202 (tt) REVERT: N 103 TYR cc_start: 0.8155 (m-10) cc_final: 0.7863 (m-10) REVERT: A 223 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 53 ASP cc_start: 0.7629 (t0) cc_final: 0.7080 (m-30) outliers start: 45 outliers final: 31 residues processed: 229 average time/residue: 0.2875 time to fit residues: 98.9714 Evaluate side-chains 222 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 6.9990 chunk 121 optimal weight: 0.0470 chunk 94 optimal weight: 0.0970 chunk 138 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16389 Z= 0.144 Angle : 0.528 6.808 22308 Z= 0.274 Chirality : 0.043 0.158 2460 Planarity : 0.004 0.053 2922 Dihedral : 4.552 42.348 2314 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.01 % Allowed : 14.79 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.24 (0.18), residues: 2118 helix: 3.19 (0.27), residues: 324 sheet: -0.97 (0.23), residues: 504 loop : -1.94 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 52 HIS 0.004 0.001 HIS I 112 PHE 0.011 0.001 PHE A 193 TYR 0.010 0.001 TYR J 88 ARG 0.008 0.000 ARG L 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 1.799 Fit side-chains REVERT: H 50 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8551 (mp) REVERT: I 7 SER cc_start: 0.6833 (p) cc_final: 0.6602 (t) REVERT: J 7 SER cc_start: 0.6754 (p) cc_final: 0.6520 (t) REVERT: L 91 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7139 (tt) REVERT: M 91 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.6950 (tt) REVERT: M 103 TYR cc_start: 0.8149 (m-10) cc_final: 0.7572 (m-10) REVERT: N 91 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7120 (tt) REVERT: N 103 TYR cc_start: 0.8150 (m-10) cc_final: 0.7806 (m-10) REVERT: A 223 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 53 ASP cc_start: 0.7707 (t0) cc_final: 0.6902 (m-30) REVERT: B 223 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8582 (p) REVERT: C 223 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (p) REVERT: C 346 MET cc_start: -0.0720 (tpt) cc_final: -0.1394 (ttp) outliers start: 33 outliers final: 22 residues processed: 233 average time/residue: 0.2844 time to fit residues: 99.4716 Evaluate side-chains 225 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 445 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0670 chunk 51 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 overall best weight: 1.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.153774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111956 restraints weight = 24984.278| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.75 r_work: 0.3263 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16389 Z= 0.208 Angle : 0.546 7.401 22308 Z= 0.283 Chirality : 0.044 0.148 2460 Planarity : 0.004 0.051 2922 Dihedral : 4.550 38.688 2312 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.37 % Allowed : 14.97 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.27 (0.18), residues: 2118 helix: 3.27 (0.27), residues: 324 sheet: -1.03 (0.23), residues: 504 loop : -1.97 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 52 HIS 0.004 0.001 HIS I 112 PHE 0.011 0.001 PHE A 125 TYR 0.025 0.001 TYR B 423 ARG 0.008 0.000 ARG L 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.31 seconds wall clock time: 82 minutes 32.85 seconds (4952.85 seconds total)