Starting phenix.real_space_refine on Tue Feb 13 21:03:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0b_29652/02_2024/8g0b_29652_updated.pdb" } resolution = 2.8 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= 0.013 sd= 0.199 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 7 7.06 5 S 26 5.16 5 C 5189 2.51 5 N 1236 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ASP 32": "OD1" <-> "OD2" Residue "5 GLU 65": "OE1" <-> "OE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 222": "OD1" <-> "OD2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 19 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "3" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "6" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "8" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1807 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "b" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 322 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "d" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 37} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "1" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.61 Number of scatterers: 7758 At special positions: 0 Unit cell: (79.31, 97.85, 83.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 7 34.99 S 26 16.00 O 1300 8.00 N 1236 7.00 C 5189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 2 sheets defined 86.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain '1' and resid 6 through 45 Processing helix chain '1' and resid 47 through 79 removed outlier: 3.709A pdb=" N GLN 1 50 " --> pdb=" O PRO 1 47 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY 1 51 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE 1 54 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) Proline residue: 1 56 - end of helix removed outlier: 3.585A pdb=" N ILE 1 59 " --> pdb=" O PRO 1 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL 1 61 " --> pdb=" O PHE 1 58 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU 1 65 " --> pdb=" O GLY 1 62 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA 1 66 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 1 68 " --> pdb=" O GLU 1 65 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 45 Processing helix chain '2' and resid 47 through 79 removed outlier: 4.374A pdb=" N GLY 2 51 " --> pdb=" O GLU 2 48 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE 2 54 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 2 55 " --> pdb=" O ARG 2 52 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 4.203A pdb=" N VAL 2 61 " --> pdb=" O PHE 2 58 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 2 65 " --> pdb=" O GLY 2 62 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE 2 69 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE 2 70 " --> pdb=" O ALA 2 67 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 2 76 " --> pdb=" O ALA 2 73 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 45 Processing helix chain '3' and resid 47 through 79 removed outlier: 3.814A pdb=" N GLN 3 50 " --> pdb=" O PRO 3 47 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY 3 51 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE 3 54 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR 3 55 " --> pdb=" O ARG 3 52 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.900A pdb=" N ILE 3 59 " --> pdb=" O PRO 3 56 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL 3 61 " --> pdb=" O PHE 3 58 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU 3 65 " --> pdb=" O GLY 3 62 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE 3 70 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 45 Processing helix chain '4' and resid 47 through 80 removed outlier: 4.690A pdb=" N GLY 4 51 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR 4 55 " --> pdb=" O ARG 4 52 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.730A pdb=" N ILE 4 59 " --> pdb=" O PRO 4 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL 4 61 " --> pdb=" O PHE 4 58 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL 4 64 " --> pdb=" O VAL 4 61 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU 4 65 " --> pdb=" O GLY 4 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA 4 66 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR 4 68 " --> pdb=" O GLU 4 65 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET 4 75 " --> pdb=" O LEU 4 72 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL 4 79 " --> pdb=" O ALA 4 76 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE 4 80 " --> pdb=" O LEU 4 77 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 45 Processing helix chain '5' and resid 48 through 80 removed outlier: 3.835A pdb=" N GLY 5 51 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE 5 54 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix removed outlier: 3.831A pdb=" N VAL 5 61 " --> pdb=" O PHE 5 58 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA 5 66 " --> pdb=" O LEU 5 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA 5 67 " --> pdb=" O VAL 5 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR 5 68 " --> pdb=" O GLU 5 65 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET 5 75 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL 5 79 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE 5 80 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 45 Processing helix chain '6' and resid 47 through 80 removed outlier: 3.749A pdb=" N GLN 6 50 " --> pdb=" O PRO 6 47 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY 6 51 " --> pdb=" O GLU 6 48 " (cutoff:3.500A) Proline residue: 6 56 - end of helix removed outlier: 3.996A pdb=" N VAL 6 61 " --> pdb=" O PHE 6 58 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL 6 64 " --> pdb=" O VAL 6 61 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU 6 65 " --> pdb=" O GLY 6 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA 6 66 " --> pdb=" O LEU 6 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA 6 67 " --> pdb=" O VAL 6 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR 6 68 " --> pdb=" O GLU 6 65 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET 6 75 " --> pdb=" O LEU 6 72 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA 6 76 " --> pdb=" O ALA 6 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL 6 79 " --> pdb=" O ALA 6 76 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE 6 80 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 45 Processing helix chain '7' and resid 47 through 49 No H-bonds generated for 'chain '7' and resid 47 through 49' Processing helix chain '7' and resid 52 through 79 Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 6 through 45 Processing helix chain '8' and resid 47 through 79 removed outlier: 3.830A pdb=" N GLN 8 50 " --> pdb=" O PRO 8 47 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY 8 51 " --> pdb=" O GLU 8 48 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.689A pdb=" N VAL 8 61 " --> pdb=" O PHE 8 58 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU 8 65 " --> pdb=" O GLY 8 62 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA 8 66 " --> pdb=" O LEU 8 63 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR 8 68 " --> pdb=" O GLU 8 65 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET 8 75 " --> pdb=" O LEU 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 45 Processing helix chain '9' and resid 47 through 80 removed outlier: 3.861A pdb=" N GLY 9 51 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU 9 53 " --> pdb=" O GLN 9 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE 9 54 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 9 55 " --> pdb=" O ARG 9 52 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.737A pdb=" N VAL 9 61 " --> pdb=" O PHE 9 58 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU 9 65 " --> pdb=" O GLY 9 62 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA 9 66 " --> pdb=" O LEU 9 63 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE 9 80 " --> pdb=" O LEU 9 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 51 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 3.775A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 153 Processing helix chain 'a' and resid 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix removed outlier: 4.025A pdb=" N GLU a 178 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.540A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY a 191 " --> pdb=" O ARG a 188 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN a 192 " --> pdb=" O LEU a 189 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE a 194 " --> pdb=" O GLY a 191 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE a 203 " --> pdb=" O VAL a 200 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 245 removed outlier: 3.922A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 4.001A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 removed outlier: 4.303A pdb=" N ILE b 36 " --> pdb=" O ALA b 33 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE b 45 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 63 Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 25 through 39 removed outlier: 4.093A pdb=" N MET d 30 " --> pdb=" O VAL d 26 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= B, first strand: chain 'a' and resid 112 through 114 667 hydrogen bonds defined for protein. 1449 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: 2.56 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2362 1.34 - 1.49: 2225 1.49 - 1.64: 3299 1.64 - 1.78: 2 1.78 - 1.93: 56 Bond restraints: 7944 Sorted by residual: bond pdb=" CA ARG d 27 " pdb=" C ARG d 27 " ideal model delta sigma weight residual 1.519 1.448 0.071 1.22e-02 6.72e+03 3.37e+01 bond pdb=" CA VAL d 26 " pdb=" C VAL d 26 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.27e-02 6.20e+03 3.37e+01 bond pdb=" N VAL d 26 " pdb=" CA VAL d 26 " ideal model delta sigma weight residual 1.459 1.401 0.058 1.25e-02 6.40e+03 2.18e+01 bond pdb=" CA THR d 28 " pdb=" C THR d 28 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.24e-02 6.50e+03 1.86e+01 bond pdb=" C THR d 28 " pdb=" O THR d 28 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.65e+01 ... (remaining 7939 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.70: 187 105.70 - 112.76: 4136 112.76 - 119.83: 2484 119.83 - 126.89: 3945 126.89 - 133.96: 70 Bond angle restraints: 10822 Sorted by residual: angle pdb=" N ARG d 27 " pdb=" CA ARG d 27 " pdb=" C ARG d 27 " ideal model delta sigma weight residual 113.55 103.83 9.72 1.26e+00 6.30e-01 5.95e+01 angle pdb=" C10 YGR 8 601 " pdb=" C07 YGR 8 601 " pdb=" O08 YGR 8 601 " ideal model delta sigma weight residual 100.25 120.69 -20.44 3.00e+00 1.11e-01 4.64e+01 angle pdb=" C10 YGR 5 601 " pdb=" C07 YGR 5 601 " pdb=" O08 YGR 5 601 " ideal model delta sigma weight residual 100.25 120.42 -20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" C10 YGR 4 601 " pdb=" C07 YGR 4 601 " pdb=" O08 YGR 4 601 " ideal model delta sigma weight residual 100.25 120.40 -20.15 3.00e+00 1.11e-01 4.51e+01 angle pdb=" C10 YGR 9 601 " pdb=" C07 YGR 9 601 " pdb=" O08 YGR 9 601 " ideal model delta sigma weight residual 100.25 120.35 -20.10 3.00e+00 1.11e-01 4.49e+01 ... (remaining 10817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.56: 4250 31.56 - 63.13: 93 63.13 - 94.69: 15 94.69 - 126.25: 0 126.25 - 157.82: 1 Dihedral angle restraints: 4359 sinusoidal: 1557 harmonic: 2802 Sorted by residual: dihedral pdb=" C33 YGR 9 601 " pdb=" C31 YGR 9 601 " pdb=" O32 YGR 9 601 " pdb=" N30 YGR 9 601 " ideal model delta sinusoidal sigma weight residual -15.35 -173.17 157.82 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C VAL d 26 " pdb=" N VAL d 26 " pdb=" CA VAL d 26 " pdb=" CB VAL d 26 " ideal model delta harmonic sigma weight residual -122.00 -113.36 -8.64 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" CB GLU a 246 " pdb=" CG GLU a 246 " pdb=" CD GLU a 246 " pdb=" OE1 GLU a 246 " ideal model delta sinusoidal sigma weight residual 0.00 89.50 -89.50 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 952 0.046 - 0.092: 263 0.092 - 0.138: 31 0.138 - 0.183: 0 0.183 - 0.229: 2 Chirality restraints: 1248 Sorted by residual: chirality pdb=" C05 YGR 8 601 " pdb=" C04 YGR 8 601 " pdb=" C06 YGR 8 601 " pdb=" C18 YGR 8 601 " both_signs ideal model delta sigma weight residual False -2.77 -2.54 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C18 YGR 8 601 " pdb=" C05 YGR 8 601 " pdb=" C19 YGR 8 601 " pdb=" C25 YGR 8 601 " both_signs ideal model delta sigma weight residual False -2.88 -2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA TYR a 145 " pdb=" N TYR a 145 " pdb=" C TYR a 145 " pdb=" CB TYR a 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1245 not shown) Planarity restraints: 1329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 1 46 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO 1 47 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO 1 47 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 1 47 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 5 46 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO 5 47 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO 5 47 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 5 47 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C05 YGR 8 601 " -0.018 2.00e-02 2.50e+03 8.56e-03 1.83e+00 pdb=" C06 YGR 8 601 " 0.012 2.00e-02 2.50e+03 pdb=" C07 YGR 8 601 " -0.001 2.00e-02 2.50e+03 pdb=" C10 YGR 8 601 " 0.003 2.00e-02 2.50e+03 pdb=" C14 YGR 8 601 " 0.004 2.00e-02 2.50e+03 pdb=" C17 YGR 8 601 " 0.009 2.00e-02 2.50e+03 pdb=" N13 YGR 8 601 " -0.006 2.00e-02 2.50e+03 pdb=" O08 YGR 8 601 " 0.009 2.00e-02 2.50e+03 pdb=" O11 YGR 8 601 " -0.007 2.00e-02 2.50e+03 pdb=" O15 YGR 8 601 " -0.004 2.00e-02 2.50e+03 ... (remaining 1326 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1553 2.76 - 3.29: 8345 3.29 - 3.83: 14233 3.83 - 4.36: 17213 4.36 - 4.90: 29281 Nonbonded interactions: 70625 Sorted by model distance: nonbonded pdb=" OE1 GLU 7 65 " pdb=" N21 YGR 7 601 " model vdw 2.221 2.520 nonbonded pdb=" OD1 ASN a 132 " pdb=" N ASN b 28 " model vdw 2.280 2.520 nonbonded pdb=" OE1 GLU 8 65 " pdb=" N21 YGR 8 601 " model vdw 2.301 2.520 nonbonded pdb=" N ASN a 28 " pdb=" OG1 THR b 30 " model vdw 2.305 2.520 nonbonded pdb=" OE1 GLU 5 65 " pdb=" N21 YGR 5 601 " model vdw 2.345 2.520 ... (remaining 70620 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 '1' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '2' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '3' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '4' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 85)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '6' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '7' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '8' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '9' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) } 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: 1.620 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: 0.000 Extract box with map and model: 7.190 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.490 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 7944 Z= 0.463 Angle : 1.119 20.439 10822 Z= 0.445 Chirality : 0.041 0.229 1248 Planarity : 0.005 0.050 1329 Dihedral : 14.699 157.816 2603 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1018 helix: 0.84 (0.18), residues: 874 sheet: -3.10 (1.56), residues: 9 loop : -1.08 (0.63), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 PHE 0.016 0.001 PHE a 142 TYR 0.009 0.001 TYR a 145 ARG 0.006 0.001 ARG b 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: d 27 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6809 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 1.0080 time to fit residues: 150.0968 Evaluate side-chains 115 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 46 GLN 6 46 GLN ** 7 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 71 ASN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7944 Z= 0.301 Angle : 0.607 7.564 10822 Z= 0.305 Chirality : 0.043 0.156 1248 Planarity : 0.005 0.048 1329 Dihedral : 10.620 120.944 1159 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 9.46 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1018 helix: 1.23 (0.18), residues: 828 sheet: -3.01 (1.60), residues: 9 loop : -0.14 (0.53), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 66 HIS 0.003 0.001 HIS a 12 PHE 0.020 0.002 PHE a 142 TYR 0.008 0.001 TYR 3 68 ARG 0.006 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: 4 65 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8286 (mm-30) REVERT: 7 69 PHE cc_start: 0.8608 (t80) cc_final: 0.8258 (t80) REVERT: a 73 MET cc_start: 0.8312 (mmt) cc_final: 0.7549 (mmt) REVERT: d 27 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6676 (tpp-160) outliers start: 12 outliers final: 4 residues processed: 125 average time/residue: 0.9919 time to fit residues: 132.9604 Evaluate side-chains 118 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 92 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 GLN 6 46 GLN 6 71 ASN 9 50 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7944 Z= 0.227 Angle : 0.562 8.312 10822 Z= 0.282 Chirality : 0.041 0.144 1248 Planarity : 0.005 0.046 1329 Dihedral : 9.832 104.498 1159 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.44 % Allowed : 10.74 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.27), residues: 1018 helix: 1.00 (0.18), residues: 898 sheet: -3.03 (1.63), residues: 9 loop : -0.95 (0.69), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 208 HIS 0.002 0.001 HIS a 12 PHE 0.020 0.001 PHE a 142 TYR 0.008 0.001 TYR a 145 ARG 0.008 0.001 ARG 8 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: 7 69 PHE cc_start: 0.8637 (t80) cc_final: 0.8423 (t80) REVERT: a 132 ASN cc_start: 0.8644 (m-40) cc_final: 0.8415 (m110) REVERT: d 27 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6682 (tpp-160) outliers start: 17 outliers final: 5 residues processed: 137 average time/residue: 1.0442 time to fit residues: 152.9250 Evaluate side-chains 122 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 71 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 46 GLN 6 46 GLN 9 50 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7944 Z= 0.244 Angle : 0.577 9.214 10822 Z= 0.289 Chirality : 0.041 0.149 1248 Planarity : 0.005 0.045 1329 Dihedral : 9.547 98.716 1159 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 12.46 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.27), residues: 1018 helix: 1.17 (0.18), residues: 883 sheet: -2.96 (1.64), residues: 9 loop : -0.63 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 208 HIS 0.002 0.001 HIS a 146 PHE 0.019 0.002 PHE a 142 TYR 0.008 0.001 TYR 1 68 ARG 0.009 0.001 ARG 8 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: 4 65 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8295 (mm-30) REVERT: 4 75 MET cc_start: 0.7815 (tmm) cc_final: 0.7540 (tmt) REVERT: 7 69 PHE cc_start: 0.8623 (t80) cc_final: 0.8306 (t80) REVERT: a 243 GLN cc_start: 0.8264 (mt0) cc_final: 0.8055 (mt0) REVERT: d 27 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6817 (tpp-160) outliers start: 15 outliers final: 5 residues processed: 126 average time/residue: 1.0057 time to fit residues: 135.7647 Evaluate side-chains 120 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 46 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7944 Z= 0.236 Angle : 0.574 9.712 10822 Z= 0.287 Chirality : 0.041 0.152 1248 Planarity : 0.005 0.045 1329 Dihedral : 9.237 90.350 1159 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.01 % Allowed : 13.90 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.27), residues: 1018 helix: 1.07 (0.18), residues: 899 sheet: -3.07 (1.61), residues: 9 loop : -0.92 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 208 HIS 0.002 0.001 HIS a 146 PHE 0.019 0.001 PHE a 142 TYR 0.008 0.001 TYR 1 68 ARG 0.011 0.001 ARG 8 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: 4 75 MET cc_start: 0.7835 (tmm) cc_final: 0.7520 (tmt) REVERT: 7 69 PHE cc_start: 0.8607 (t80) cc_final: 0.8303 (t80) REVERT: 8 65 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7301 (mm-30) REVERT: d 27 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6852 (tpp-160) outliers start: 14 outliers final: 5 residues processed: 131 average time/residue: 1.0278 time to fit residues: 144.0756 Evaluate side-chains 121 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7944 Z= 0.202 Angle : 0.560 9.480 10822 Z= 0.279 Chirality : 0.040 0.150 1248 Planarity : 0.005 0.047 1329 Dihedral : 8.858 83.449 1159 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.29 % Allowed : 13.90 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1018 helix: 1.17 (0.18), residues: 899 sheet: -3.07 (1.64), residues: 9 loop : -1.02 (0.69), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 208 HIS 0.002 0.001 HIS a 146 PHE 0.020 0.001 PHE a 142 TYR 0.037 0.001 TYR a 145 ARG 0.010 0.001 ARG 8 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8532 (mm) REVERT: 4 65 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8305 (mm-30) REVERT: a 205 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7880 (mtm) REVERT: d 27 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6866 (tpp-160) outliers start: 16 outliers final: 5 residues processed: 134 average time/residue: 0.9713 time to fit residues: 139.6202 Evaluate side-chains 128 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 55 optimal weight: 0.0030 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 6 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7944 Z= 0.183 Angle : 0.554 10.954 10822 Z= 0.275 Chirality : 0.040 0.162 1248 Planarity : 0.005 0.044 1329 Dihedral : 8.483 87.437 1159 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.15 % Allowed : 15.62 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.27), residues: 1018 helix: 1.23 (0.18), residues: 899 sheet: -3.09 (1.62), residues: 9 loop : -1.00 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.001 PHE a 142 TYR 0.034 0.001 TYR a 145 ARG 0.008 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.794 Fit side-chains REVERT: 1 63 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8481 (mm) REVERT: 4 75 MET cc_start: 0.7754 (tmm) cc_final: 0.7498 (tmt) REVERT: a 205 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7704 (mtt) REVERT: d 27 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6938 (tpp-160) outliers start: 15 outliers final: 5 residues processed: 136 average time/residue: 1.0059 time to fit residues: 146.7752 Evaluate side-chains 128 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 6 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 GLN 5 46 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7944 Z= 0.229 Angle : 0.585 11.988 10822 Z= 0.290 Chirality : 0.041 0.181 1248 Planarity : 0.006 0.098 1329 Dihedral : 8.372 87.681 1159 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.01 % Allowed : 16.19 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.27), residues: 1018 helix: 1.19 (0.18), residues: 899 sheet: -3.13 (1.60), residues: 9 loop : -1.06 (0.69), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE a 142 TYR 0.040 0.002 TYR a 145 ARG 0.008 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.780 Fit side-chains REVERT: 1 63 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8496 (mm) REVERT: 5 21 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7582 (mmm) REVERT: a 205 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7734 (mtt) outliers start: 14 outliers final: 5 residues processed: 126 average time/residue: 0.9924 time to fit residues: 134.1847 Evaluate side-chains 124 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 21 MET Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain b residue 63 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 0.0040 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 ASN 3 6 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7944 Z= 0.221 Angle : 0.586 12.471 10822 Z= 0.292 Chirality : 0.041 0.188 1248 Planarity : 0.005 0.072 1329 Dihedral : 8.089 85.119 1155 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.29 % Allowed : 16.19 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1018 helix: 1.18 (0.18), residues: 899 sheet: -3.10 (1.62), residues: 9 loop : -1.10 (0.68), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE a 142 TYR 0.040 0.002 TYR a 145 ARG 0.012 0.001 ARG 3 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.898 Fit side-chains REVERT: 1 63 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8467 (mm) REVERT: a 205 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7725 (mtt) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.9671 time to fit residues: 130.8094 Evaluate side-chains 129 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 21 MET Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain b residue 63 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 ASN 3 6 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 GLN 9 50 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7944 Z= 0.235 Angle : 0.582 12.818 10822 Z= 0.292 Chirality : 0.042 0.187 1248 Planarity : 0.005 0.062 1329 Dihedral : 8.120 87.806 1155 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.29 % Allowed : 16.05 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1018 helix: 1.15 (0.18), residues: 899 sheet: -3.09 (1.61), residues: 9 loop : -1.09 (0.67), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE a 142 TYR 0.014 0.001 TYR 4 68 ARG 0.012 0.001 ARG 3 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.786 Fit side-chains REVERT: 1 63 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8486 (mm) REVERT: a 205 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7736 (mtt) REVERT: a 243 GLN cc_start: 0.8441 (mt0) cc_final: 0.8228 (mt0) outliers start: 16 outliers final: 9 residues processed: 122 average time/residue: 1.0546 time to fit residues: 137.7908 Evaluate side-chains 128 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 21 MET Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain b residue 63 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 6 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 GLN 9 50 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115377 restraints weight = 6312.921| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.00 r_work: 0.3256 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7944 Z= 0.257 Angle : 0.607 12.523 10822 Z= 0.304 Chirality : 0.042 0.187 1248 Planarity : 0.006 0.070 1329 Dihedral : 8.076 78.488 1155 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.72 % Allowed : 16.91 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.27), residues: 1018 helix: 1.18 (0.18), residues: 890 sheet: -3.02 (1.61), residues: 9 loop : -1.54 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.017 0.001 PHE 6 74 TYR 0.041 0.002 TYR a 145 ARG 0.018 0.001 ARG 8 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.30 seconds wall clock time: 51 minutes 57.03 seconds (3117.03 seconds total)