Starting phenix.real_space_refine on Thu Jan 18 02:23:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648_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/8g07_29648/01_2024/8g07_29648_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g07_29648/01_2024/8g07_29648_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= 0.014 sd= 0.169 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 27 5.16 5 C 4978 2.51 5 N 1212 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 65": "OE1" <-> "OE2" Residue "3 ASP 32": "OD1" <-> "OD2" Residue "8 PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7467 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" 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: "2" 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: "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: 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: "5" 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: "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: 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: "a" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1808 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "b" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 312 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "d" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 295 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 37} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "9" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'SQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.58, per 1000 atoms: 0.61 Number of scatterers: 7467 At special positions: 0 Unit cell: (89.61, 76.22, 84.46, 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 27 16.00 O 1250 8.00 N 1212 7.00 C 4978 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: 3.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 2 sheets defined 86.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain '1' and resid 6 through 45 Processing helix chain '1' and resid 47 through 80 removed outlier: 4.039A pdb=" N LEU 1 53 " --> pdb=" O GLN 1 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE 1 54 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 1 55 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) Proline residue: 1 56 - end of helix removed outlier: 3.825A pdb=" N VAL 1 61 " --> pdb=" O PHE 1 58 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU 1 65 " --> pdb=" O GLY 1 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA 1 66 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA 1 67 " --> pdb=" O VAL 1 64 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE 1 70 " --> pdb=" O ALA 1 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU 1 77 " --> pdb=" O PHE 1 74 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE 1 80 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 45 Processing helix chain '2' and resid 47 through 80 removed outlier: 3.537A pdb=" N GLN 2 50 " --> pdb=" O PRO 2 47 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY 2 51 " --> pdb=" O GLU 2 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE 2 54 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR 2 55 " --> pdb=" O ARG 2 52 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 3.757A pdb=" N ILE 2 59 " --> pdb=" O PRO 2 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL 2 61 " --> pdb=" O PHE 2 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU 2 65 " --> pdb=" O GLY 2 62 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE 2 70 " --> pdb=" O ALA 2 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET 2 75 " --> pdb=" O LEU 2 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 2 77 " --> pdb=" O PHE 2 74 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 2 79 " --> pdb=" O ALA 2 76 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE 2 80 " --> pdb=" O LEU 2 77 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 45 Processing helix chain '3' and resid 47 through 79 removed outlier: 3.925A pdb=" N GLN 3 50 " --> pdb=" O PRO 3 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY 3 51 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE 3 54 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR 3 55 " --> pdb=" O ARG 3 52 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.538A pdb=" N ILE 3 59 " --> pdb=" O PRO 3 56 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 3 61 " --> pdb=" O PHE 3 58 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU 3 65 " --> pdb=" O GLY 3 62 " (cutoff:3.500A) removed outlier: 3.955A 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: 3.835A pdb=" N GLN 4 50 " --> pdb=" O PRO 4 47 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY 4 51 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 4 53 " --> pdb=" O GLN 4 50 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE 4 54 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR 4 55 " --> pdb=" O ARG 4 52 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.665A pdb=" N MET 4 75 " --> pdb=" O LEU 4 72 " (cutoff:3.500A) removed outlier: 4.055A 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 47 through 79 removed outlier: 3.816A pdb=" N GLN 5 50 " --> pdb=" O PRO 5 47 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY 5 51 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE 5 54 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR 5 55 " --> pdb=" O ARG 5 52 " (cutoff:3.500A) Proline residue: 5 56 - end of helix removed outlier: 3.755A pdb=" N VAL 5 61 " --> pdb=" O PHE 5 58 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE 5 70 " --> pdb=" O ALA 5 67 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 45 Processing helix chain '6' and resid 47 through 79 removed outlier: 3.579A pdb=" N GLN 6 50 " --> pdb=" O PRO 6 47 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY 6 51 " --> pdb=" O GLU 6 48 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE 6 54 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR 6 55 " --> pdb=" O ARG 6 52 " (cutoff:3.500A) Proline residue: 6 56 - end of helix removed outlier: 3.675A pdb=" N ILE 6 59 " --> pdb=" O PRO 6 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL 6 61 " --> pdb=" O PHE 6 58 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU 6 65 " --> pdb=" O GLY 6 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE 6 70 " --> pdb=" O ALA 6 67 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE 6 74 " --> pdb=" O ASN 6 71 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 45 Processing helix chain '7' and resid 48 through 79 removed outlier: 3.828A pdb=" N LEU 7 53 " --> pdb=" O GLN 7 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE 7 54 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR 7 55 " --> pdb=" O ARG 7 52 " (cutoff:3.500A) Proline residue: 7 56 - end of helix removed outlier: 3.586A pdb=" N ILE 7 59 " --> pdb=" O PRO 7 56 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL 7 61 " --> pdb=" O PHE 7 58 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU 7 65 " --> pdb=" O GLY 7 62 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA 7 67 " --> pdb=" O VAL 7 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE 7 70 " --> pdb=" O ALA 7 67 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 45 Processing helix chain '8' and resid 47 through 79 removed outlier: 3.505A pdb=" N GLN 8 50 " --> pdb=" O PRO 8 47 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY 8 51 " --> pdb=" O GLU 8 48 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR 8 55 " --> pdb=" O ARG 8 52 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.658A pdb=" N ILE 8 59 " --> pdb=" O PRO 8 56 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL 8 61 " --> pdb=" O PHE 8 58 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU 8 65 " --> pdb=" O GLY 8 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 8 70 " --> pdb=" O ALA 8 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 73 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 45 Processing helix chain '9' and resid 47 through 79 removed outlier: 4.098A pdb=" N LEU 9 53 " --> pdb=" O GLN 9 50 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE 9 54 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR 9 55 " --> pdb=" O ARG 9 52 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.569A pdb=" N ILE 9 59 " --> pdb=" O PRO 9 56 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL 9 61 " --> pdb=" O PHE 9 58 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA 9 67 " --> pdb=" O VAL 9 64 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE 9 70 " --> pdb=" O ALA 9 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN 9 71 " --> pdb=" O TYR 9 68 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL 9 79 " --> pdb=" O ALA 9 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 52 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 3.576A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR a 95 " --> pdb=" O PRO a 91 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 3.919A 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 171 through 205 removed outlier: 3.634A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU a 177 " --> pdb=" O ILE a 173 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.828A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.561A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.977A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE b 36 " --> pdb=" O ALA b 33 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE b 45 " --> pdb=" O LEU b 42 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS b 47 " --> pdb=" O VAL b 44 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP b 48 " --> pdb=" O ILE b 45 " (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 23 through 39 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 114 671 hydrogen bonds defined for protein. 1470 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: 2.38 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1165 1.28 - 1.41: 1918 1.41 - 1.54: 4487 1.54 - 1.68: 10 1.68 - 1.81: 53 Bond restraints: 7633 Sorted by residual: bond pdb=" C PHE a 221 " pdb=" O PHE a 221 " ideal model delta sigma weight residual 1.237 1.144 0.093 1.17e-02 7.31e+03 6.28e+01 bond pdb=" C ASN 5 6 " pdb=" O ASN 5 6 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.17e-02 7.31e+03 6.03e+01 bond pdb=" N GLN 4 46 " pdb=" CA GLN 4 46 " ideal model delta sigma weight residual 1.464 1.390 0.073 1.09e-02 8.42e+03 4.50e+01 bond pdb=" C ASN 4 6 " pdb=" O ASN 4 6 " ideal model delta sigma weight residual 1.237 1.159 0.078 1.17e-02 7.31e+03 4.45e+01 bond pdb=" C ALA 9 66 " pdb=" O ALA 9 66 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.15e-02 7.56e+03 4.29e+01 ... (remaining 7628 not shown) Histogram of bond angle deviations from ideal: 89.59 - 98.93: 5 98.93 - 108.27: 314 108.27 - 117.61: 5276 117.61 - 126.95: 4708 126.95 - 136.29: 75 Bond angle restraints: 10378 Sorted by residual: angle pdb=" C GLN 6 46 " pdb=" N PRO 6 47 " pdb=" CA PRO 6 47 " ideal model delta sigma weight residual 119.84 111.35 8.49 1.25e+00 6.40e-01 4.61e+01 angle pdb=" N THR d 28 " pdb=" CA THR d 28 " pdb=" C THR d 28 " ideal model delta sigma weight residual 110.97 104.31 6.66 1.09e+00 8.42e-01 3.73e+01 angle pdb=" N ALA 9 66 " pdb=" CA ALA 9 66 " pdb=" C ALA 9 66 " ideal model delta sigma weight residual 110.97 104.55 6.42 1.09e+00 8.42e-01 3.46e+01 angle pdb=" N VAL d 26 " pdb=" CA VAL d 26 " pdb=" C VAL d 26 " ideal model delta sigma weight residual 110.62 104.79 5.83 1.02e+00 9.61e-01 3.27e+01 angle pdb=" C06 SQC 9 601 " pdb=" C07 SQC 9 601 " pdb=" N08 SQC 9 601 " ideal model delta sigma weight residual 103.72 120.33 -16.61 3.00e+00 1.11e-01 3.07e+01 ... (remaining 10373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 3802 15.84 - 31.69: 370 31.69 - 47.53: 68 47.53 - 63.37: 29 63.37 - 79.22: 10 Dihedral angle restraints: 4279 sinusoidal: 1474 harmonic: 2805 Sorted by residual: dihedral pdb=" C ALA 9 66 " pdb=" N ALA 9 66 " pdb=" CA ALA 9 66 " pdb=" CB ALA 9 66 " ideal model delta harmonic sigma weight residual -122.60 -111.73 -10.87 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" CA PHE 9 80 " pdb=" C PHE 9 80 " pdb=" N ALA 9 81 " pdb=" CA ALA 9 81 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" N GLN 4 46 " pdb=" C GLN 4 46 " pdb=" CA GLN 4 46 " pdb=" CB GLN 4 46 " ideal model delta harmonic sigma weight residual 122.80 113.21 9.59 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 4276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 949 0.048 - 0.096: 241 0.096 - 0.144: 36 0.144 - 0.192: 8 0.192 - 0.240: 1 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CB VAL 9 64 " pdb=" CA VAL 9 64 " pdb=" CG1 VAL 9 64 " pdb=" CG2 VAL 9 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU 8 72 " pdb=" N LEU 8 72 " pdb=" C LEU 8 72 " pdb=" CB LEU 8 72 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA PRO 6 47 " pdb=" N PRO 6 47 " pdb=" C PRO 6 47 " pdb=" CB PRO 6 47 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1232 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA 3 76 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ALA 3 76 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA 3 76 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU 3 77 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY a 197 " -0.013 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLY a 197 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY a 197 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE a 198 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 4 69 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C PHE 4 69 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE 4 69 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE 4 70 " 0.014 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1856 2.78 - 3.31: 8208 3.31 - 3.84: 13759 3.84 - 4.37: 16617 4.37 - 4.90: 28063 Nonbonded interactions: 68503 Sorted by model distance: nonbonded pdb=" OG SER a 55 " pdb=" OE1 GLU b 59 " model vdw 2.253 2.440 nonbonded pdb=" O GLN a 72 " pdb=" OE1 GLN a 76 " model vdw 2.299 3.040 nonbonded pdb=" O PHE a 99 " pdb=" OG SER a 103 " model vdw 2.304 2.440 nonbonded pdb=" OD1 ASP a 30 " pdb=" N THR a 31 " model vdw 2.314 2.520 nonbonded pdb=" O ALA 6 76 " pdb=" N PHE 6 80 " model vdw 2.354 2.520 ... (remaining 68498 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 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 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 '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 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 '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 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 '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 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)) } 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.470 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.710 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.008 0.102 7633 Z= 0.521 Angle : 0.813 16.612 10378 Z= 0.481 Chirality : 0.043 0.240 1235 Planarity : 0.005 0.057 1309 Dihedral : 14.124 79.219 2521 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.15 % Allowed : 2.31 % Favored : 96.54 % Cbeta Deviations : 0.11 % 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: 1.07 (0.27), residues: 1019 helix: 1.07 (0.18), residues: 843 sheet: -1.97 (1.47), residues: 9 loop : -0.67 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.012 0.001 PHE 6 74 TYR 0.014 0.001 TYR a 145 ARG 0.007 0.001 ARG 7 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.773 Fit side-chains REVERT: 4 21 MET cc_start: 0.7539 (mmm) cc_final: 0.7272 (mmm) REVERT: 4 45 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6860 (tmt170) REVERT: 7 58 PHE cc_start: 0.7971 (m-80) cc_final: 0.7706 (m-80) REVERT: a 73 MET cc_start: 0.7829 (mmt) cc_final: 0.7146 (mmt) REVERT: a 210 ILE cc_start: 0.7473 (mm) cc_final: 0.7261 (mm) outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 1.0212 time to fit residues: 136.0033 Evaluate side-chains 92 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 45 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN 7 46 GLN 9 46 GLN 9 50 GLN a 72 GLN a 215 ASN d 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7633 Z= 0.229 Angle : 0.546 6.618 10378 Z= 0.290 Chirality : 0.040 0.196 1235 Planarity : 0.005 0.042 1309 Dihedral : 5.850 81.028 1088 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.16 % Allowed : 10.37 % Favored : 87.46 % 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: 1.41 (0.27), residues: 1019 helix: 1.29 (0.18), residues: 846 sheet: -1.89 (1.48), residues: 9 loop : -0.43 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 48 HIS 0.004 0.001 HIS a 146 PHE 0.023 0.002 PHE a 194 TYR 0.025 0.001 TYR a 145 ARG 0.006 0.001 ARG 1 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.774 Fit side-chains REVERT: 3 52 ARG cc_start: 0.8520 (ptt180) cc_final: 0.8307 (ptt180) REVERT: 4 45 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6577 (tpt90) REVERT: 7 58 PHE cc_start: 0.7958 (m-80) cc_final: 0.7675 (m-80) REVERT: a 73 MET cc_start: 0.7887 (mmt) cc_final: 0.7015 (mmt) REVERT: a 75 GLN cc_start: 0.7887 (mt0) cc_final: 0.7665 (mt0) outliers start: 15 outliers final: 5 residues processed: 107 average time/residue: 1.1620 time to fit residues: 131.8705 Evaluate side-chains 93 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 6 residue 8 ILE Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.0470 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN 7 46 GLN a 63 GLN a 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7633 Z= 0.188 Angle : 0.492 6.333 10378 Z= 0.260 Chirality : 0.039 0.129 1235 Planarity : 0.005 0.042 1309 Dihedral : 5.585 72.968 1088 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.88 % Allowed : 11.82 % Favored : 85.30 % 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: 1.63 (0.27), residues: 1019 helix: 1.43 (0.18), residues: 845 sheet: -1.81 (1.52), residues: 9 loop : -0.33 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE a 194 TYR 0.023 0.001 TYR a 145 ARG 0.004 0.000 ARG 1 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.711 Fit side-chains REVERT: 4 21 MET cc_start: 0.7627 (mmm) cc_final: 0.7423 (mmm) REVERT: 4 45 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6544 (tpt90) REVERT: 5 45 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6553 (ttm-80) REVERT: 7 58 PHE cc_start: 0.7912 (m-80) cc_final: 0.7618 (m-80) REVERT: a 74 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7672 (ttp80) REVERT: a 76 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7587 (mp10) outliers start: 20 outliers final: 4 residues processed: 105 average time/residue: 1.1332 time to fit residues: 126.2246 Evaluate side-chains 92 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU 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: 0.7980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN 7 46 GLN 9 50 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 GLN a 112 GLN a 215 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7633 Z= 0.256 Angle : 0.523 6.456 10378 Z= 0.276 Chirality : 0.040 0.138 1235 Planarity : 0.005 0.044 1309 Dihedral : 5.601 70.736 1088 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.74 % Allowed : 12.97 % Favored : 84.29 % 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: 1.49 (0.26), residues: 1019 helix: 1.33 (0.18), residues: 844 sheet: -1.84 (1.52), residues: 9 loop : -0.36 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.002 PHE 6 74 TYR 0.023 0.001 TYR a 145 ARG 0.006 0.001 ARG 2 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.707 Fit side-chains REVERT: 2 21 MET cc_start: 0.7371 (mmm) cc_final: 0.6921 (tpt) REVERT: 4 45 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6656 (tmt170) REVERT: 5 45 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6551 (ttm-80) REVERT: 7 58 PHE cc_start: 0.7950 (m-80) cc_final: 0.7668 (m-80) REVERT: a 74 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7691 (ttp80) REVERT: a 76 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: d 27 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6035 (ttm-80) outliers start: 19 outliers final: 6 residues processed: 107 average time/residue: 1.1569 time to fit residues: 131.1717 Evaluate side-chains 102 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU 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: 0.9980 chunk 56 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 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** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 71 ASN 7 46 GLN ** 7 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 50 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7633 Z= 0.217 Angle : 0.502 6.442 10378 Z= 0.267 Chirality : 0.039 0.125 1235 Planarity : 0.005 0.043 1309 Dihedral : 5.527 67.570 1088 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.74 % Allowed : 13.26 % Favored : 84.01 % 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: 1.50 (0.26), residues: 1019 helix: 1.34 (0.18), residues: 844 sheet: -1.72 (1.52), residues: 9 loop : -0.35 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 48 HIS 0.008 0.001 HIS a 16 PHE 0.022 0.001 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.007 0.001 ARG 2 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.773 Fit side-chains REVERT: 2 21 MET cc_start: 0.7421 (mmm) cc_final: 0.6979 (tpt) REVERT: 4 45 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6629 (tmt170) REVERT: 5 45 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6590 (ttm-80) REVERT: 7 58 PHE cc_start: 0.7934 (m-80) cc_final: 0.7642 (m-80) REVERT: a 50 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6041 (ttm170) REVERT: a 73 MET cc_start: 0.7866 (mmt) cc_final: 0.6974 (mmt) REVERT: a 76 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: d 27 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.6031 (ttm-80) outliers start: 19 outliers final: 5 residues processed: 104 average time/residue: 1.1046 time to fit residues: 121.7009 Evaluate side-chains 100 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU 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: 0.5980 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 7 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 50 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7633 Z= 0.228 Angle : 0.509 6.467 10378 Z= 0.270 Chirality : 0.039 0.125 1235 Planarity : 0.005 0.044 1309 Dihedral : 5.497 64.796 1088 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.88 % Allowed : 12.97 % Favored : 84.15 % 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: 1.49 (0.26), residues: 1019 helix: 1.33 (0.18), residues: 844 sheet: -1.56 (1.55), residues: 9 loop : -0.35 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 48 HIS 0.006 0.001 HIS a 16 PHE 0.020 0.001 PHE 1 69 TYR 0.022 0.001 TYR a 145 ARG 0.006 0.001 ARG 2 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.752 Fit side-chains REVERT: 2 21 MET cc_start: 0.7453 (mmm) cc_final: 0.7023 (tpt) REVERT: 4 45 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6661 (tmt170) REVERT: 5 45 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6604 (ttm-80) REVERT: 6 45 ARG cc_start: 0.7366 (ttm-80) cc_final: 0.7044 (ttp-110) REVERT: 7 58 PHE cc_start: 0.7937 (m-80) cc_final: 0.7657 (m-80) REVERT: a 50 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6089 (ttm170) REVERT: a 74 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7681 (ttp80) REVERT: a 76 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: d 27 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5971 (ttm-80) outliers start: 20 outliers final: 6 residues processed: 105 average time/residue: 1.1681 time to fit residues: 129.6695 Evaluate side-chains 100 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 61 VAL Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU 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: 0.1980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 45 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 9 50 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7633 Z= 0.183 Angle : 0.492 6.438 10378 Z= 0.260 Chirality : 0.038 0.124 1235 Planarity : 0.005 0.046 1309 Dihedral : 5.386 59.917 1088 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.03 % Allowed : 13.26 % Favored : 83.72 % 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: 1.64 (0.27), residues: 1019 helix: 1.43 (0.18), residues: 846 sheet: -1.54 (1.56), residues: 9 loop : -0.29 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 48 HIS 0.006 0.001 HIS a 16 PHE 0.018 0.001 PHE 1 69 TYR 0.022 0.001 TYR a 145 ARG 0.011 0.001 ARG 1 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.832 Fit side-chains REVERT: 2 21 MET cc_start: 0.7477 (mmm) cc_final: 0.7055 (tpt) REVERT: 4 45 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6412 (tpt90) REVERT: 5 45 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6606 (ttm-80) REVERT: 6 45 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7060 (ttp-110) REVERT: a 50 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6103 (ttm170) REVERT: a 76 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7576 (mp10) outliers start: 21 outliers final: 5 residues processed: 108 average time/residue: 1.2028 time to fit residues: 137.4504 Evaluate side-chains 102 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 61 VAL Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.0570 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.1980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7633 Z= 0.182 Angle : 0.494 6.456 10378 Z= 0.260 Chirality : 0.038 0.127 1235 Planarity : 0.005 0.044 1309 Dihedral : 5.277 57.423 1088 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.59 % Allowed : 14.41 % Favored : 83.00 % 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: 1.77 (0.27), residues: 1019 helix: 1.50 (0.18), residues: 847 sheet: -1.52 (1.57), residues: 9 loop : -0.13 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 48 HIS 0.006 0.001 HIS a 16 PHE 0.018 0.001 PHE 6 74 TYR 0.023 0.001 TYR a 145 ARG 0.008 0.001 ARG 2 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.715 Fit side-chains REVERT: 2 21 MET cc_start: 0.7472 (mmm) cc_final: 0.7053 (tpt) REVERT: 2 75 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: 4 45 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6426 (tmt170) REVERT: 5 45 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6674 (ttm-80) REVERT: 6 45 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7058 (ttp-110) REVERT: a 76 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7568 (mp10) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 1.1485 time to fit residues: 129.2094 Evaluate side-chains 103 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 3 residue 61 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.0470 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 28 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 97 optimal weight: 0.0370 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7633 Z= 0.157 Angle : 0.490 7.588 10378 Z= 0.254 Chirality : 0.038 0.124 1235 Planarity : 0.005 0.043 1309 Dihedral : 5.112 56.883 1088 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.87 % Allowed : 15.71 % Favored : 82.42 % 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: 2.02 (0.27), residues: 1019 helix: 1.67 (0.18), residues: 847 sheet: -1.55 (1.57), residues: 9 loop : 0.01 (0.56), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 48 HIS 0.005 0.001 HIS a 16 PHE 0.016 0.001 PHE a 194 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.001 ARG 2 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.732 Fit side-chains REVERT: 2 21 MET cc_start: 0.7344 (mmm) cc_final: 0.6946 (tpt) REVERT: 2 75 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7309 (tmm) REVERT: 5 45 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6608 (ptm160) REVERT: 6 45 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.7058 (ttp-110) REVERT: a 52 LYS cc_start: 0.8174 (tttt) cc_final: 0.7940 (mmmt) REVERT: a 76 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: b 48 TRP cc_start: 0.7335 (m-10) cc_final: 0.6977 (m-90) outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 1.0449 time to fit residues: 118.0163 Evaluate side-chains 104 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7633 Z= 0.232 Angle : 0.519 6.525 10378 Z= 0.274 Chirality : 0.039 0.123 1235 Planarity : 0.005 0.046 1309 Dihedral : 4.762 53.923 1084 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.31 % Allowed : 15.85 % Favored : 81.84 % 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: 1.78 (0.26), residues: 1019 helix: 1.50 (0.18), residues: 845 sheet: -1.56 (1.57), residues: 9 loop : -0.01 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.007 0.001 HIS a 16 PHE 0.028 0.002 PHE 4 74 TYR 0.023 0.001 TYR a 145 ARG 0.006 0.001 ARG 2 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.831 Fit side-chains REVERT: 2 21 MET cc_start: 0.7458 (mmm) cc_final: 0.7048 (tpt) REVERT: 2 75 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7510 (tmm) REVERT: 5 45 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6597 (ptm160) REVERT: 6 71 ASN cc_start: 0.8117 (m-40) cc_final: 0.7882 (m110) REVERT: a 76 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: b 48 TRP cc_start: 0.7430 (m-10) cc_final: 0.7057 (m-90) outliers start: 16 outliers final: 6 residues processed: 104 average time/residue: 1.0431 time to fit residues: 115.6725 Evaluate side-chains 105 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 3 residue 61 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116129 restraints weight = 8502.313| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.62 r_work: 0.3341 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7633 Z= 0.195 Angle : 0.503 6.462 10378 Z= 0.268 Chirality : 0.039 0.124 1235 Planarity : 0.005 0.046 1309 Dihedral : 4.781 53.957 1084 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.73 % Allowed : 16.86 % Favored : 81.41 % 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: 1.82 (0.26), residues: 1019 helix: 1.60 (0.17), residues: 836 sheet: -1.50 (1.59), residues: 9 loop : -0.38 (0.53), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS a 146 PHE 0.022 0.001 PHE 5 74 TYR 0.023 0.001 TYR a 145 ARG 0.007 0.001 ARG 1 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.75 seconds wall clock time: 60 minutes 28.73 seconds (3628.73 seconds total)