Starting phenix.real_space_refine on Thu Nov 16 18:12:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/11_2023/7tz5_26202_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/11_2023/7tz5_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_26202/11_2023/7tz5_26202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/11_2023/7tz5_26202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/11_2023/7tz5_26202_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz5_26202/11_2023/7tz5_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-1.21rc1-5144/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: 8.45, per 1000 atoms: 0.53 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: 5.81 Conformation dependent library (CDL) restraints added in 2.8 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: 1.97 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: 5.35 Time building geometry restraints manager: 6.36 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: 8.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 28.470 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 43.080 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 84.060 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.782 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 230 average time/residue: 0.2793 time to fit residues: 95.8957 Evaluate side-chains 188 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.1408 time to fit residues: 4.0099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 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: I 44 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16389 Z= 0.202 Angle : 0.645 6.385 22308 Z= 0.347 Chirality : 0.047 0.194 2460 Planarity : 0.004 0.040 2922 Dihedral : 5.407 39.396 2307 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.52 % Allowed : 6.57 % Favored : 91.91 % 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: -1.62 (0.17), residues: 2118 helix: 2.49 (0.26), residues: 324 sheet: -1.16 (0.22), residues: 510 loop : -2.10 (0.15), residues: 1284 *********************** 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 246 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 2.114 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 231 average time/residue: 0.3024 time to fit residues: 102.1760 Evaluate side-chains 208 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 14 average time/residue: 0.1369 time to fit residues: 6.1548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 chunk 191 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ** 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: 0.8002 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16389 Z= 0.237 Angle : 0.589 5.650 22308 Z= 0.314 Chirality : 0.045 0.146 2460 Planarity : 0.004 0.041 2922 Dihedral : 5.089 35.757 2307 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.31 % Allowed : 8.76 % Favored : 88.92 % 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: -1.37 (0.17), residues: 2118 helix: 2.88 (0.26), residues: 321 sheet: -0.94 (0.22), residues: 510 loop : -2.02 (0.16), residues: 1287 *********************** 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 243 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 205 time to evaluate : 1.829 Fit side-chains outliers start: 38 outliers final: 13 residues processed: 233 average time/residue: 0.3002 time to fit residues: 103.0072 Evaluate side-chains 204 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 13 average time/residue: 0.1401 time to fit residues: 5.9155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 0.2980 chunk 191 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 HIS ** 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 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 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16389 Z= 0.301 Angle : 0.597 6.854 22308 Z= 0.317 Chirality : 0.046 0.172 2460 Planarity : 0.004 0.040 2922 Dihedral : 5.071 35.747 2307 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.25 % Allowed : 11.56 % Favored : 86.18 % 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: -1.39 (0.18), residues: 2118 helix: 3.01 (0.28), residues: 324 sheet: -1.01 (0.22), residues: 504 loop : -2.05 (0.16), residues: 1290 *********************** 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 232 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 2.108 Fit side-chains outliers start: 37 outliers final: 14 residues processed: 223 average time/residue: 0.2880 time to fit residues: 96.2943 Evaluate side-chains 189 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.909 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 14 average time/residue: 0.1431 time to fit residues: 6.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.8047 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16389 Z= 0.276 Angle : 0.579 7.206 22308 Z= 0.307 Chirality : 0.045 0.225 2460 Planarity : 0.004 0.040 2922 Dihedral : 4.946 32.113 2307 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.95 % Allowed : 12.78 % Favored : 85.27 % 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: -1.38 (0.18), residues: 2118 helix: 3.03 (0.28), residues: 324 sheet: -1.00 (0.22), residues: 501 loop : -2.05 (0.16), residues: 1293 *********************** 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 209 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 2.087 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 203 average time/residue: 0.3001 time to fit residues: 91.1898 Evaluate side-chains 191 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 5 residues processed: 19 average time/residue: 0.1479 time to fit residues: 7.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN ** 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** N 44 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16389 Z= 0.269 Angle : 0.575 6.427 22308 Z= 0.303 Chirality : 0.045 0.231 2460 Planarity : 0.004 0.040 2922 Dihedral : 4.878 32.869 2307 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.77 % Allowed : 13.02 % Favored : 85.21 % 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: -1.40 (0.18), residues: 2118 helix: 3.07 (0.28), residues: 324 sheet: -1.03 (0.22), residues: 501 loop : -2.07 (0.16), residues: 1293 *********************** 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 216 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 2.281 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 207 average time/residue: 0.3100 time to fit residues: 95.5651 Evaluate side-chains 195 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 14 average time/residue: 0.1407 time to fit residues: 6.2606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN ** 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** N 44 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16389 Z= 0.215 Angle : 0.553 6.475 22308 Z= 0.291 Chirality : 0.044 0.205 2460 Planarity : 0.004 0.040 2922 Dihedral : 4.698 23.956 2307 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.16 % Allowed : 13.94 % Favored : 84.91 % 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: -1.39 (0.18), residues: 2118 helix: 3.13 (0.27), residues: 324 sheet: -1.07 (0.22), residues: 504 loop : -2.06 (0.16), residues: 1290 *********************** 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 205 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 2.006 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 203 average time/residue: 0.2980 time to fit residues: 89.5421 Evaluate side-chains 186 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 11 average time/residue: 0.1397 time to fit residues: 5.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 475 ASN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16389 Z= 0.374 Angle : 0.625 6.415 22308 Z= 0.328 Chirality : 0.047 0.208 2460 Planarity : 0.004 0.042 2922 Dihedral : 4.995 26.372 2307 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 1.28 % Allowed : 14.30 % Favored : 84.42 % 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: -1.62 (0.18), residues: 2118 helix: 2.92 (0.28), residues: 324 sheet: -1.23 (0.22), residues: 498 loop : -2.21 (0.15), residues: 1296 *********************** 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 208 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.955 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 202 average time/residue: 0.3045 time to fit residues: 91.4254 Evaluate side-chains 194 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 12 average time/residue: 0.1411 time to fit residues: 5.8017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 40.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16389 Z= 0.216 Angle : 0.570 7.288 22308 Z= 0.298 Chirality : 0.045 0.196 2460 Planarity : 0.004 0.051 2922 Dihedral : 4.785 31.879 2307 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.67 % Allowed : 14.61 % Favored : 84.72 % 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: -1.52 (0.18), residues: 2118 helix: 3.02 (0.28), residues: 324 sheet: -1.26 (0.22), residues: 507 loop : -2.10 (0.16), residues: 1287 *********************** 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 199 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 1.884 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 199 average time/residue: 0.3100 time to fit residues: 91.0758 Evaluate side-chains 188 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.1413 time to fit residues: 4.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.1980 chunk 121 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16389 Z= 0.167 Angle : 0.541 6.329 22308 Z= 0.283 Chirality : 0.044 0.186 2460 Planarity : 0.004 0.050 2922 Dihedral : 4.481 23.528 2307 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.37 % Allowed : 15.46 % Favored : 84.18 % 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: -1.40 (0.18), residues: 2118 helix: 3.10 (0.27), residues: 324 sheet: -1.26 (0.22), residues: 513 loop : -1.97 (0.16), residues: 1281 ********************** 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 216 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 1.921 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 216 average time/residue: 0.2976 time to fit residues: 95.3741 Evaluate side-chains 192 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.998 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.1427 time to fit residues: 4.0212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 210 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 = 0.3866 r_free = 0.3866 target = 0.149324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107203 restraints weight = 25234.897| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.74 r_work: 0.3200 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16389 Z= 0.412 Angle : 0.645 7.630 22308 Z= 0.337 Chirality : 0.047 0.202 2460 Planarity : 0.004 0.047 2922 Dihedral : 4.913 26.528 2307 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.85 % Allowed : 15.82 % Favored : 83.32 % 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: -1.62 (0.18), residues: 2118 helix: 2.95 (0.28), residues: 324 sheet: -1.45 (0.22), residues: 516 loop : -2.10 (0.16), residues: 1278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4226.22 seconds wall clock time: 77 minutes 44.75 seconds (4664.75 seconds total)