Starting phenix.real_space_refine on Thu Mar 14 23:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soy_40671/03_2024/8soy_40671.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soy_40671/03_2024/8soy_40671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soy_40671/03_2024/8soy_40671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soy_40671/03_2024/8soy_40671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soy_40671/03_2024/8soy_40671.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soy_40671/03_2024/8soy_40671.pdb" } resolution = 2.85 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= 0.003 sd= 0.159 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 30 5.16 5 C 6390 2.51 5 N 1801 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "F ASP 165": "OD1" <-> "OD2" Residue "F ASP 177": "OD1" <-> "OD2" Residue "F ASP 179": "OD1" <-> "OD2" Residue "F GLU 209": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1679 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1663 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1684 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1683 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 56 Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1690 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 5.55, per 1000 atoms: 0.55 Number of scatterers: 10074 At special positions: 0 Unit cell: (86.86, 89.44, 97.18, 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 30 16.00 O 1853 8.00 N 1801 7.00 C 6390 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: 3.58 Conformation dependent library (CDL) restraints added in 1.9 seconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 12 sheets defined 58.3% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.782A pdb=" N ASP A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 229 through 248 removed outlier: 3.713A pdb=" N VAL A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 Proline residue: B 39 - end of helix removed outlier: 3.709A pdb=" N PHE B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.524A pdb=" N ASP B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 164 through 175 Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 195 through 211 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 229 through 248 removed outlier: 3.681A pdb=" N VAL B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.927A pdb=" N ALA B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 Proline residue: C 39 - end of helix removed outlier: 3.530A pdb=" N LEU C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 removed outlier: 3.549A pdb=" N ASP C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.696A pdb=" N ARG C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 195 through 211 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.638A pdb=" N ALA C 219 " --> pdb=" O PRO C 215 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 248 removed outlier: 3.796A pdb=" N VAL C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.940A pdb=" N ALA C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.576A pdb=" N TRP D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 82 through 105 removed outlier: 3.784A pdb=" N ASP D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 229 through 248 removed outlier: 3.714A pdb=" N VAL D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.899A pdb=" N ALA D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 46 removed outlier: 3.796A pdb=" N TRP E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) Proline residue: E 39 - end of helix Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.577A pdb=" N ASP E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 96 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 127 Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 195 through 211 removed outlier: 3.838A pdb=" N SER E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.778A pdb=" N ALA E 219 " --> pdb=" O PRO E 215 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 248 removed outlier: 3.792A pdb=" N VAL E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.896A pdb=" N ALA E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 48 Proline residue: F 39 - end of helix removed outlier: 3.636A pdb=" N PHE F 42 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 105 removed outlier: 3.903A pdb=" N ASP F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 100 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 164 through 175 Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 195 through 212 removed outlier: 3.702A pdb=" N SER F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS F 204 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 227 removed outlier: 3.700A pdb=" N ALA F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 248 removed outlier: 3.761A pdb=" N VAL F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.894A pdb=" N ALA F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 4.557A pdb=" N GLY A 58 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 131 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 191 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 8 through 12 removed outlier: 4.579A pdb=" N GLY B 58 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 131 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 191 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 13 removed outlier: 4.584A pdb=" N GLY C 58 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 131 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 135 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP C 191 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 117 through 119 removed outlier: 6.855A pdb=" N CYS C 118 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 8 through 13 removed outlier: 4.555A pdb=" N GLY D 58 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 131 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP D 191 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AA9, first strand: chain 'E' and resid 8 through 12 removed outlier: 4.569A pdb=" N GLY E 58 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 131 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 135 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP E 191 " --> pdb=" O ARG E 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 117 through 119 removed outlier: 6.801A pdb=" N CYS E 118 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 8 through 12 removed outlier: 4.561A pdb=" N GLY F 58 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 131 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP F 191 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 117 through 119 611 hydrogen bonds defined for protein. 1770 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: 2.97 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3355 1.34 - 1.46: 1298 1.46 - 1.57: 5535 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 10236 Sorted by residual: bond pdb=" C LEU A 159 " pdb=" N PRO A 160 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.19e-02 7.06e+03 4.00e+00 bond pdb=" CG LEU A 21 " pdb=" CD1 LEU A 21 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CG LEU F 21 " pdb=" CD1 LEU F 21 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" CG LEU C 21 " pdb=" CD1 LEU C 21 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CG LEU E 21 " pdb=" CD1 LEU E 21 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 ... (remaining 10231 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 275 107.15 - 113.86: 5927 113.86 - 120.58: 3988 120.58 - 127.30: 3665 127.30 - 134.02: 105 Bond angle restraints: 13960 Sorted by residual: angle pdb=" CB ARG A 92 " pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " ideal model delta sigma weight residual 111.30 117.24 -5.94 2.30e+00 1.89e-01 6.68e+00 angle pdb=" N PRO A 160 " pdb=" CA PRO A 160 " pdb=" C PRO A 160 " ideal model delta sigma weight residual 113.84 117.06 -3.22 1.30e+00 5.92e-01 6.13e+00 angle pdb=" CA LEU E 21 " pdb=" CB LEU E 21 " pdb=" CG LEU E 21 " ideal model delta sigma weight residual 116.30 124.96 -8.66 3.50e+00 8.16e-02 6.12e+00 angle pdb=" CA LEU C 21 " pdb=" CB LEU C 21 " pdb=" CG LEU C 21 " ideal model delta sigma weight residual 116.30 124.92 -8.62 3.50e+00 8.16e-02 6.06e+00 angle pdb=" CA ALA B 211 " pdb=" C ALA B 211 " pdb=" N ALA B 212 " ideal model delta sigma weight residual 118.59 122.25 -3.66 1.63e+00 3.76e-01 5.04e+00 ... (remaining 13955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.47: 5462 14.47 - 28.94: 442 28.94 - 43.41: 133 43.41 - 57.89: 11 57.89 - 72.36: 8 Dihedral angle restraints: 6056 sinusoidal: 1994 harmonic: 4062 Sorted by residual: dihedral pdb=" CA ALA A 246 " pdb=" C ALA A 246 " pdb=" N PHE A 247 " pdb=" CA PHE A 247 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA VAL B 142 " pdb=" C VAL B 142 " pdb=" N ARG B 143 " pdb=" CA ARG B 143 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ALA C 246 " pdb=" C ALA C 246 " pdb=" N PHE C 247 " pdb=" CA PHE C 247 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 960 0.039 - 0.077: 535 0.077 - 0.116: 140 0.116 - 0.154: 73 0.154 - 0.193: 2 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CB VAL C 153 " pdb=" CA VAL C 153 " pdb=" CG1 VAL C 153 " pdb=" CG2 VAL C 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA PRO A 160 " pdb=" N PRO A 160 " pdb=" C PRO A 160 " pdb=" CB PRO A 160 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA VAL E 142 " pdb=" N VAL E 142 " pdb=" C VAL E 142 " pdb=" CB VAL E 142 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1707 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 159 " -0.051 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PRO B 160 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 115 " -0.020 2.00e-02 2.50e+03 2.46e-02 9.10e+00 pdb=" CG HIS E 115 " 0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS E 115 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS E 115 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS E 115 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 115 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 159 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO D 160 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " 0.040 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3504 2.88 - 3.38: 8740 3.38 - 3.89: 15804 3.89 - 4.39: 17515 4.39 - 4.90: 31507 Nonbonded interactions: 77070 Sorted by model distance: nonbonded pdb=" O GLU A 170 " pdb=" OG1 THR A 174 " model vdw 2.374 2.440 nonbonded pdb=" O GLU F 170 " pdb=" OG1 THR F 174 " model vdw 2.382 2.440 nonbonded pdb=" OD2 ASP C 130 " pdb=" NZ LYS C 222 " model vdw 2.406 2.520 nonbonded pdb=" O GLU C 170 " pdb=" OG1 THR C 174 " model vdw 2.436 2.440 nonbonded pdb=" OE1 GLN D 18 " pdb=" NE2 HIS D 204 " model vdw 2.469 2.520 ... (remaining 77065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 83 or (resid 84 throug \ h 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 92 through 129 or (resid 130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 131 through 184 or (resid 185 and (name N or name CA or name \ C or name O or name CB )) or resid 186 through 193 or (resid 194 through 196 and \ (name N or name CA or name C or name O or name CB )) or resid 197 through 231 o \ r (resid 232 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 33 through 256)) selection = (chain 'B' and (resid 5 through 83 or (resid 84 through 85 and (name N or name C \ A or name C or name O or name CB )) or resid 86 through 90 or (resid 91 and (nam \ e N or name CA or name C or name O or name CB )) or resid 92 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 136 or (resid 137 through 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 164 or (resid 165 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 184 or (resid 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 25 \ 6)) selection = (chain 'C' and (resid 5 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 129 or (resid 130 and \ (name N or name CA or name C or name O or name CB )) or resid 131 through 231 or \ (resid 232 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 3 through 256)) selection = (chain 'D' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 83 or (resid 84 throug \ h 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 92 through 94 or (resid 95 and (name N or name CA or name C or name O or nam \ e CB )) or resid 96 through 136 or (resid 137 through 138 and (name N or name CA \ or name C or name O or name CB )) or resid 139 through 164 or (resid 165 and (n \ ame N or name CA or name C or name O or name CB )) or resid 166 through 184 or ( \ resid 185 and (name N or name CA or name C or name O or name CB )) or resid 186 \ through 231 or (resid 232 and (name N or name CA or name C or name O or name CB \ )) or resid 233 through 249 or (resid 250 through 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 through 256)) selection = (chain 'E' and (resid 5 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 67 or (resid 68 through 81 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 82 through 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 86 through 90 or (res \ id 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throu \ gh 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or r \ esid 96 through 129 or (resid 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 through 136 or (resid 137 through 138 and (name N or nam \ e CA or name C or name O or name CB )) or resid 139 through 184 or (resid 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 through 231 \ or (resid 232 and (name N or name CA or name C or name O or name CB )) or resid \ 233 through 249 or (resid 250 through 251 and (name N or name CA or name C or na \ me O or name CB )) or resid 252 through 256)) selection = (chain 'F' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 45 or (resid 46 through 48 and (nam \ e N or name CA or name C or name O or name CB )) or resid 49 through 84 or (resi \ d 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 92 through 94 or (resid 95 and (name N or name CA or name C or name O or nam \ e CB )) or resid 96 through 129 or (resid 130 and (name N or name CA or name C o \ r name O or name CB )) or resid 131 through 136 or (resid 137 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 164 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 184 or (resid 185 and (name N or name CA or name C or name O or name CB \ )) or resid 186 through 231 or (resid 232 and (name N or name CA or name C or na \ me O or name CB )) or resid 233 through 249 or (resid 250 through 251 and (name \ N or name CA or name C or name O or name CB )) or resid 252 through 256)) } 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: 0.890 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.730 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.380 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.040 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.005 0.052 10236 Z= 0.361 Angle : 0.726 8.656 13960 Z= 0.395 Chirality : 0.052 0.193 1710 Planarity : 0.007 0.077 1786 Dihedral : 12.140 72.357 3428 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.69 (0.21), residues: 1386 helix: 0.20 (0.19), residues: 702 sheet: 1.16 (0.35), residues: 180 loop : -2.00 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 243 HIS 0.030 0.003 HIS E 115 PHE 0.018 0.003 PHE D 42 TYR 0.015 0.001 TYR C 65 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 1.1840 time to fit residues: 183.4523 Evaluate side-chains 128 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN C 190 ASN F 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10236 Z= 0.262 Angle : 0.616 7.708 13960 Z= 0.341 Chirality : 0.047 0.142 1710 Planarity : 0.006 0.074 1786 Dihedral : 4.752 18.057 1500 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.99 % Allowed : 8.74 % Favored : 88.27 % 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: -0.46 (0.22), residues: 1386 helix: 0.36 (0.19), residues: 738 sheet: 1.42 (0.33), residues: 180 loop : -2.09 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 243 HIS 0.008 0.002 HIS E 115 PHE 0.015 0.002 PHE D 42 TYR 0.005 0.001 TYR B 65 ARG 0.003 0.001 ARG D 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.156 Fit side-chains REVERT: E 137 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6772 (p0) REVERT: F 130 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7091 (m-30) REVERT: F 223 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7657 (t70) outliers start: 28 outliers final: 14 residues processed: 148 average time/residue: 1.0066 time to fit residues: 161.7055 Evaluate side-chains 146 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN B 90 HIS F 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10236 Z= 0.284 Angle : 0.626 8.053 13960 Z= 0.347 Chirality : 0.048 0.144 1710 Planarity : 0.006 0.073 1786 Dihedral : 4.796 18.010 1500 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.62 % Allowed : 13.54 % Favored : 82.84 % 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: -0.44 (0.22), residues: 1386 helix: 0.35 (0.19), residues: 738 sheet: 1.53 (0.33), residues: 180 loop : -2.05 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 117 HIS 0.005 0.001 HIS B 90 PHE 0.017 0.002 PHE D 42 TYR 0.007 0.001 TYR D 65 ARG 0.003 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.111 Fit side-chains REVERT: C 200 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8321 (tt) REVERT: E 137 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6800 (p0) REVERT: E 200 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8331 (tt) REVERT: F 223 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7809 (t70) outliers start: 34 outliers final: 16 residues processed: 147 average time/residue: 1.0724 time to fit residues: 171.1194 Evaluate side-chains 145 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10236 Z= 0.163 Angle : 0.501 6.581 13960 Z= 0.276 Chirality : 0.044 0.133 1710 Planarity : 0.005 0.065 1786 Dihedral : 4.278 16.690 1500 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.41 % Allowed : 16.31 % Favored : 80.28 % 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: 0.14 (0.22), residues: 1386 helix: 0.85 (0.20), residues: 738 sheet: 1.91 (0.33), residues: 180 loop : -1.92 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 117 HIS 0.004 0.001 HIS E 90 PHE 0.013 0.002 PHE A 42 TYR 0.003 0.001 TYR B 65 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.024 Fit side-chains REVERT: E 137 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6689 (p0) REVERT: E 200 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8193 (tt) REVERT: F 223 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7549 (t70) outliers start: 32 outliers final: 10 residues processed: 158 average time/residue: 0.9962 time to fit residues: 171.4481 Evaluate side-chains 148 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.0370 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN D 115 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10236 Z= 0.320 Angle : 0.654 7.994 13960 Z= 0.361 Chirality : 0.049 0.145 1710 Planarity : 0.006 0.070 1786 Dihedral : 4.854 17.628 1500 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.26 % Allowed : 16.52 % Favored : 79.21 % 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: -0.30 (0.22), residues: 1386 helix: 0.42 (0.19), residues: 738 sheet: 1.72 (0.32), residues: 180 loop : -1.98 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 117 HIS 0.005 0.001 HIS A 115 PHE 0.018 0.002 PHE D 42 TYR 0.008 0.001 TYR D 65 ARG 0.004 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.067 Fit side-chains REVERT: E 137 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6807 (p0) REVERT: E 200 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8345 (tt) outliers start: 40 outliers final: 20 residues processed: 148 average time/residue: 0.9730 time to fit residues: 156.8893 Evaluate side-chains 148 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS D 115 HIS F 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10236 Z= 0.259 Angle : 0.600 7.472 13960 Z= 0.332 Chirality : 0.047 0.140 1710 Planarity : 0.006 0.067 1786 Dihedral : 4.708 17.335 1500 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.84 % Allowed : 18.76 % Favored : 77.40 % 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: -0.24 (0.22), residues: 1386 helix: 0.48 (0.19), residues: 738 sheet: 1.76 (0.32), residues: 180 loop : -1.98 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 117 HIS 0.005 0.001 HIS E 90 PHE 0.016 0.002 PHE D 42 TYR 0.007 0.001 TYR D 65 ARG 0.003 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.069 Fit side-chains REVERT: C 200 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8195 (tt) REVERT: E 137 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6756 (p0) REVERT: E 200 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8306 (tt) REVERT: F 30 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7591 (mtm) outliers start: 36 outliers final: 19 residues processed: 148 average time/residue: 0.9924 time to fit residues: 160.0369 Evaluate side-chains 148 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 228 GLN C 115 HIS D 115 HIS D 228 GLN E 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10236 Z= 0.440 Angle : 0.771 8.707 13960 Z= 0.425 Chirality : 0.054 0.156 1710 Planarity : 0.007 0.071 1786 Dihedral : 5.281 18.442 1500 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.44 % Allowed : 17.59 % Favored : 76.97 % 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: -0.85 (0.21), residues: 1386 helix: -0.05 (0.18), residues: 738 sheet: 1.35 (0.31), residues: 180 loop : -2.12 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 117 HIS 0.008 0.002 HIS A 115 PHE 0.021 0.003 PHE D 42 TYR 0.011 0.002 TYR D 65 ARG 0.005 0.001 ARG F 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 1.103 Fit side-chains REVERT: C 232 GLN cc_start: 0.7506 (pt0) cc_final: 0.7236 (pt0) REVERT: D 30 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7114 (ptt) REVERT: D 38 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7387 (tpt) REVERT: E 137 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6827 (p0) REVERT: E 232 GLN cc_start: 0.7513 (pt0) cc_final: 0.7256 (pt0) REVERT: F 30 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7505 (mtm) outliers start: 51 outliers final: 30 residues processed: 158 average time/residue: 1.0180 time to fit residues: 174.6465 Evaluate side-chains 161 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10236 Z= 0.278 Angle : 0.624 7.647 13960 Z= 0.345 Chirality : 0.048 0.180 1710 Planarity : 0.006 0.069 1786 Dihedral : 4.869 17.673 1500 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.69 % Allowed : 18.98 % Favored : 76.33 % 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: -0.53 (0.21), residues: 1386 helix: 0.22 (0.19), residues: 738 sheet: 1.63 (0.32), residues: 180 loop : -2.07 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 117 HIS 0.006 0.002 HIS B 115 PHE 0.017 0.002 PHE D 42 TYR 0.008 0.001 TYR B 65 ARG 0.003 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.061 Fit side-chains REVERT: E 137 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6784 (p0) REVERT: E 200 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8319 (tt) REVERT: F 30 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7531 (mtm) outliers start: 44 outliers final: 30 residues processed: 156 average time/residue: 1.0144 time to fit residues: 172.6109 Evaluate side-chains 156 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10236 Z= 0.446 Angle : 0.778 8.818 13960 Z= 0.429 Chirality : 0.054 0.176 1710 Planarity : 0.008 0.072 1786 Dihedral : 5.346 18.450 1500 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.44 % Allowed : 18.55 % Favored : 76.01 % 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: -0.98 (0.21), residues: 1386 helix: -0.17 (0.18), residues: 738 sheet: 1.30 (0.32), residues: 180 loop : -2.17 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 117 HIS 0.009 0.002 HIS A 115 PHE 0.021 0.003 PHE D 42 TYR 0.012 0.002 TYR B 65 ARG 0.005 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 125 time to evaluate : 1.081 Fit side-chains REVERT: C 232 GLN cc_start: 0.7497 (pt0) cc_final: 0.7224 (pt0) REVERT: E 137 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6828 (p0) REVERT: E 232 GLN cc_start: 0.7513 (pt0) cc_final: 0.7251 (pt0) REVERT: F 30 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7448 (mtm) outliers start: 51 outliers final: 39 residues processed: 158 average time/residue: 1.0146 time to fit residues: 174.0470 Evaluate side-chains 166 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS C 204 HIS E 94 GLN F 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10236 Z= 0.166 Angle : 0.512 6.740 13960 Z= 0.282 Chirality : 0.044 0.148 1710 Planarity : 0.005 0.066 1786 Dihedral : 4.415 16.975 1500 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.09 % Allowed : 21.22 % Favored : 75.69 % 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: -0.09 (0.22), residues: 1386 helix: 0.64 (0.19), residues: 738 sheet: 1.91 (0.33), residues: 180 loop : -2.02 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 117 HIS 0.005 0.001 HIS B 115 PHE 0.014 0.002 PHE D 42 TYR 0.005 0.001 TYR B 65 ARG 0.002 0.000 ARG F 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.251 Fit side-chains REVERT: B 12 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7965 (t) REVERT: D 12 VAL cc_start: 0.8335 (p) cc_final: 0.8063 (t) REVERT: E 137 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6596 (p0) REVERT: E 200 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8208 (tt) REVERT: F 30 MET cc_start: 0.7798 (ptp) cc_final: 0.7379 (mtm) outliers start: 29 outliers final: 15 residues processed: 153 average time/residue: 0.9829 time to fit residues: 163.6998 Evaluate side-chains 150 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS C 204 HIS D 115 HIS F 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.181046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.169719 restraints weight = 9541.399| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 0.64 r_work: 0.3688 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10236 Z= 0.220 Angle : 0.563 7.232 13960 Z= 0.309 Chirality : 0.046 0.159 1710 Planarity : 0.005 0.064 1786 Dihedral : 4.559 17.118 1500 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.09 % Allowed : 22.07 % Favored : 74.84 % 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: -0.05 (0.22), residues: 1386 helix: 0.64 (0.19), residues: 738 sheet: 1.98 (0.33), residues: 180 loop : -1.98 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 117 HIS 0.006 0.001 HIS B 115 PHE 0.016 0.002 PHE A 42 TYR 0.005 0.001 TYR B 65 ARG 0.002 0.000 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3221.60 seconds wall clock time: 57 minutes 42.93 seconds (3462.93 seconds total)