Starting phenix.real_space_refine on Sun Apr 14 06:00:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijk_35487/04_2024/8ijk_35487_neut_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians S 88 5.16 5 C 9972 2.51 5 N 2580 2.21 5 O 2696 1.98 5 F 4 1.80 5 H 15016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 140": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30356 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.06, per 1000 atoms: 0.43 Number of scatterers: 30356 At special positions: 0 Unit cell: (129.27, 129.27, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 F 4 9.00 O 2696 8.00 N 2580 7.00 C 9972 6.00 H 15016 1.00 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: 24.61 Conformation dependent library (CDL) restraints added in 2.9 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 91 through 114 Processing helix chain 'A' and resid 119 through 148 removed outlier: 3.892A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.944A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 254 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 348 removed outlier: 4.429A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Proline residue: A 308 - end of helix Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 536 through 558 Processing helix chain 'A' and resid 564 through 599 removed outlier: 3.597A pdb=" N GLY A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) Proline residue: A 597 - end of helix Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 119 through 148 removed outlier: 3.893A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.945A pdb=" N ARG B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 254 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 348 removed outlier: 4.428A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Proline residue: B 308 - end of helix Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 536 through 558 Processing helix chain 'B' and resid 564 through 599 removed outlier: 3.599A pdb=" N GLY B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 91 through 114 Processing helix chain 'C' and resid 119 through 148 removed outlier: 3.890A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 removed outlier: 3.949A pdb=" N ARG C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 254 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'C' and resid 288 through 348 removed outlier: 4.428A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Proline residue: C 308 - end of helix Proline residue: C 335 - end of helix Processing helix chain 'C' and resid 536 through 558 Processing helix chain 'C' and resid 564 through 599 removed outlier: 3.598A pdb=" N GLY C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) Proline residue: C 597 - end of helix Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 91 through 114 Processing helix chain 'D' and resid 119 through 148 removed outlier: 3.893A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.950A pdb=" N ARG D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 161 " --> pdb=" O TRP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 253 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 348 removed outlier: 4.428A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) Proline residue: D 308 - end of helix Proline residue: D 335 - end of helix Processing helix chain 'D' and resid 536 through 558 Processing helix chain 'D' and resid 564 through 599 removed outlier: 3.599A pdb=" N GLY D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Proline residue: D 597 - end of helix Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 77 through 80 No H-bonds generated for 'chain 'E' and resid 77 through 80' Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'F' and resid 77 through 80 No H-bonds generated for 'chain 'F' and resid 77 through 80' Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 30 through 40 Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 66 through 73 Processing helix chain 'G' and resid 77 through 80 No H-bonds generated for 'chain 'G' and resid 77 through 80' Processing helix chain 'G' and resid 83 through 93 Processing helix chain 'G' and resid 103 through 112 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 77 through 80 No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 147 1089 hydrogen bonds defined for protein. 3267 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: 11.10 Time building geometry restraints manager: 25.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14988 1.03 - 1.23: 146 1.23 - 1.43: 6530 1.43 - 1.62: 8868 1.62 - 1.82: 148 Bond restraints: 30680 Sorted by residual: bond pdb=" C16 7PN A 801 " pdb=" C17 7PN A 801 " ideal model delta sigma weight residual 1.385 1.524 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C16 7PN B 801 " pdb=" C17 7PN B 801 " ideal model delta sigma weight residual 1.385 1.523 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C16 7PN C 801 " pdb=" C17 7PN C 801 " ideal model delta sigma weight residual 1.385 1.522 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C16 7PN D 801 " pdb=" C17 7PN D 801 " ideal model delta sigma weight residual 1.385 1.522 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C14 7PN D 801 " pdb=" C15 7PN D 801 " ideal model delta sigma weight residual 1.385 1.521 -0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 30675 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.56: 148 104.56 - 111.97: 34187 111.97 - 119.39: 7792 119.39 - 126.80: 12906 126.80 - 134.22: 179 Bond angle restraints: 55212 Sorted by residual: angle pdb=" C12 7PN D 801 " pdb=" C6 7PN D 801 " pdb=" N1 7PN D 801 " ideal model delta sigma weight residual 91.91 121.49 -29.58 3.00e+00 1.11e-01 9.72e+01 angle pdb=" C12 7PN C 801 " pdb=" C6 7PN C 801 " pdb=" N1 7PN C 801 " ideal model delta sigma weight residual 91.91 121.41 -29.50 3.00e+00 1.11e-01 9.67e+01 angle pdb=" C12 7PN B 801 " pdb=" C6 7PN B 801 " pdb=" N1 7PN B 801 " ideal model delta sigma weight residual 91.91 121.38 -29.47 3.00e+00 1.11e-01 9.65e+01 angle pdb=" C12 7PN A 801 " pdb=" C6 7PN A 801 " pdb=" N1 7PN A 801 " ideal model delta sigma weight residual 91.91 121.38 -29.47 3.00e+00 1.11e-01 9.65e+01 angle pdb=" C5 7PN D 801 " pdb=" C2 7PN D 801 " pdb=" C6 7PN D 801 " ideal model delta sigma weight residual 108.12 125.62 -17.50 3.00e+00 1.11e-01 3.40e+01 ... (remaining 55207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12404 17.92 - 35.85: 1274 35.85 - 53.77: 405 53.77 - 71.70: 107 71.70 - 89.62: 34 Dihedral angle restraints: 14224 sinusoidal: 7564 harmonic: 6660 Sorted by residual: dihedral pdb=" CA TRP A 91 " pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " pdb=" CD1 TRP A 91 " ideal model delta sinusoidal sigma weight residual 90.00 158.09 -68.09 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA TRP B 91 " pdb=" CB TRP B 91 " pdb=" CG TRP B 91 " pdb=" CD1 TRP B 91 " ideal model delta sinusoidal sigma weight residual 90.00 158.09 -68.09 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA TRP C 91 " pdb=" CB TRP C 91 " pdb=" CG TRP C 91 " pdb=" CD1 TRP C 91 " ideal model delta sinusoidal sigma weight residual 90.00 158.00 -68.00 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 14221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1521 0.027 - 0.054: 591 0.054 - 0.081: 162 0.081 - 0.108: 51 0.108 - 0.135: 11 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA PRO C 308 " pdb=" N PRO C 308 " pdb=" C PRO C 308 " pdb=" CB PRO C 308 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA PRO D 308 " pdb=" N PRO D 308 " pdb=" C PRO D 308 " pdb=" CB PRO D 308 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2333 not shown) Planarity restraints: 4532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 66 " 0.053 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO E 67 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.053 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO H 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 66 " 0.052 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO F 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 67 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 67 " 0.043 5.00e-02 4.00e+02 ... (remaining 4529 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1137 2.13 - 2.75: 56801 2.75 - 3.36: 93267 3.36 - 3.98: 108851 3.98 - 4.60: 173157 Nonbonded interactions: 433213 Sorted by model distance: nonbonded pdb=" OD1 ASN G 138 " pdb=" H GLU G 140 " model vdw 1.510 1.850 nonbonded pdb=" OD1 ASN H 138 " pdb=" H GLU H 140 " model vdw 1.511 1.850 nonbonded pdb=" OD1 ASN F 138 " pdb=" H GLU F 140 " model vdw 1.511 1.850 nonbonded pdb=" OD1 ASN E 138 " pdb=" H GLU E 140 " model vdw 1.512 1.850 nonbonded pdb="HH12 ARG G 38 " pdb=" O GLN G 42 " model vdw 1.566 1.850 ... (remaining 433208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.440 Extract box with map and model: 4.610 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 95.660 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.190 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.006 0.139 15664 Z= 0.433 Angle : 0.810 29.577 21084 Z= 0.382 Chirality : 0.033 0.135 2336 Planarity : 0.004 0.076 2664 Dihedral : 17.412 89.619 5612 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.75 % Allowed : 22.64 % Favored : 76.62 % 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: 2.03 (0.19), residues: 1888 helix: 1.83 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 146 HIS 0.002 0.001 HIS C 228 PHE 0.011 0.001 PHE D 548 TYR 0.012 0.001 TYR A 74 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6727 (mm-30) cc_final: 0.5452 (tt0) REVERT: D 140 GLU cc_start: 0.6718 (mm-30) cc_final: 0.5433 (tt0) REVERT: E 52 MET cc_start: 0.7630 (mtt) cc_final: 0.7401 (mtt) REVERT: G 52 MET cc_start: 0.7637 (mtt) cc_final: 0.7411 (mtt) outliers start: 12 outliers final: 10 residues processed: 241 average time/residue: 0.6848 time to fit residues: 232.5193 Evaluate side-chains 190 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15664 Z= 0.206 Angle : 0.667 14.914 21084 Z= 0.313 Chirality : 0.031 0.127 2336 Planarity : 0.003 0.035 2664 Dihedral : 6.215 79.177 2046 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.55 % Allowed : 21.77 % Favored : 76.68 % 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: 2.32 (0.19), residues: 1888 helix: 2.05 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.001 0.000 HIS B 260 PHE 0.013 0.001 PHE B 240 TYR 0.010 0.001 TYR D 74 ARG 0.003 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7381 (ptt) cc_final: 0.7172 (ptp) REVERT: C 140 GLU cc_start: 0.6727 (mm-30) cc_final: 0.5552 (tt0) REVERT: D 140 GLU cc_start: 0.6741 (mm-30) cc_final: 0.5542 (tt0) outliers start: 25 outliers final: 13 residues processed: 217 average time/residue: 0.7325 time to fit residues: 222.8666 Evaluate side-chains 191 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15664 Z= 0.250 Angle : 0.664 14.817 21084 Z= 0.319 Chirality : 0.031 0.137 2336 Planarity : 0.003 0.035 2664 Dihedral : 5.503 79.694 2032 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.74 % Allowed : 21.95 % Favored : 76.31 % 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: 2.24 (0.19), residues: 1888 helix: 1.98 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.003 0.001 HIS C 260 PHE 0.012 0.001 PHE C 240 TYR 0.013 0.001 TYR A 74 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 546 MET cc_start: 0.8146 (tpp) cc_final: 0.7940 (tpp) REVERT: C 140 GLU cc_start: 0.6776 (mm-30) cc_final: 0.5563 (tt0) REVERT: D 140 GLU cc_start: 0.6782 (mm-30) cc_final: 0.5568 (tt0) REVERT: D 546 MET cc_start: 0.8158 (tpp) cc_final: 0.7955 (tpp) REVERT: E 52 MET cc_start: 0.7552 (mtt) cc_final: 0.7340 (mtt) REVERT: F 52 MET cc_start: 0.7498 (mtt) cc_final: 0.7182 (mtt) REVERT: G 52 MET cc_start: 0.7557 (mtt) cc_final: 0.7344 (mtt) REVERT: H 52 MET cc_start: 0.7502 (mtt) cc_final: 0.7186 (mtt) outliers start: 28 outliers final: 21 residues processed: 211 average time/residue: 0.7167 time to fit residues: 219.2440 Evaluate side-chains 202 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15664 Z= 0.180 Angle : 0.642 15.068 21084 Z= 0.298 Chirality : 0.031 0.123 2336 Planarity : 0.003 0.033 2664 Dihedral : 5.424 78.464 2032 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.93 % Allowed : 21.52 % Favored : 76.55 % 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: 2.56 (0.20), residues: 1888 helix: 2.19 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 344 HIS 0.001 0.000 HIS B 260 PHE 0.014 0.001 PHE C 240 TYR 0.007 0.001 TYR A 74 ARG 0.004 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 546 MET cc_start: 0.7963 (tpp) cc_final: 0.7610 (tpp) REVERT: C 140 GLU cc_start: 0.6782 (mm-30) cc_final: 0.5647 (tt0) REVERT: D 140 GLU cc_start: 0.6786 (mm-30) cc_final: 0.5649 (tt0) REVERT: D 546 MET cc_start: 0.7971 (tpp) cc_final: 0.7635 (tpp) REVERT: E 52 MET cc_start: 0.7618 (mtt) cc_final: 0.7271 (mtt) REVERT: F 75 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7500 (tpp80) REVERT: G 52 MET cc_start: 0.7622 (mtt) cc_final: 0.7262 (mtt) REVERT: G 75 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7498 (tpp80) outliers start: 31 outliers final: 26 residues processed: 224 average time/residue: 0.7614 time to fit residues: 235.6780 Evaluate side-chains 216 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 15664 Z= 0.439 Angle : 0.742 15.062 21084 Z= 0.379 Chirality : 0.035 0.163 2336 Planarity : 0.004 0.038 2664 Dihedral : 6.080 89.947 2032 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.92 % Allowed : 20.52 % Favored : 75.56 % 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: 1.84 (0.19), residues: 1888 helix: 1.70 (0.12), residues: 1536 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 146 HIS 0.005 0.001 HIS C 260 PHE 0.017 0.002 PHE D 548 TYR 0.022 0.002 TYR B 74 ARG 0.003 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 192 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6623 (mm-30) cc_final: 0.5493 (tt0) REVERT: D 140 GLU cc_start: 0.6610 (mm-30) cc_final: 0.5469 (tt0) REVERT: E 52 MET cc_start: 0.7765 (mtt) cc_final: 0.7334 (mtt) REVERT: F 146 MET cc_start: 0.8654 (tmm) cc_final: 0.8433 (tmm) REVERT: G 52 MET cc_start: 0.7769 (mtt) cc_final: 0.7339 (mtt) REVERT: G 146 MET cc_start: 0.8649 (tmm) cc_final: 0.8432 (tmm) outliers start: 63 outliers final: 37 residues processed: 247 average time/residue: 0.6700 time to fit residues: 236.9089 Evaluate side-chains 222 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15664 Z= 0.208 Angle : 0.663 14.987 21084 Z= 0.313 Chirality : 0.031 0.131 2336 Planarity : 0.003 0.034 2664 Dihedral : 5.921 87.851 2032 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.80 % Allowed : 21.58 % Favored : 75.62 % 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: 2.22 (0.19), residues: 1888 helix: 1.95 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.71 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 344 HIS 0.001 0.000 HIS C 328 PHE 0.012 0.001 PHE D 240 TYR 0.010 0.001 TYR B 74 ARG 0.004 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8256 (tpp) cc_final: 0.8029 (tpp) REVERT: C 140 GLU cc_start: 0.6737 (mm-30) cc_final: 0.5526 (tt0) REVERT: D 140 GLU cc_start: 0.6805 (mm-30) cc_final: 0.5581 (tt0) REVERT: E 52 MET cc_start: 0.7586 (mtt) cc_final: 0.7173 (mtt) REVERT: F 75 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7373 (tpp80) REVERT: F 146 MET cc_start: 0.8594 (tmm) cc_final: 0.8354 (tmm) REVERT: G 75 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7342 (tpp80) REVERT: G 146 MET cc_start: 0.8586 (tmm) cc_final: 0.8351 (tmm) outliers start: 45 outliers final: 37 residues processed: 234 average time/residue: 0.6800 time to fit residues: 226.5125 Evaluate side-chains 232 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15664 Z= 0.205 Angle : 0.663 14.938 21084 Z= 0.312 Chirality : 0.031 0.128 2336 Planarity : 0.003 0.036 2664 Dihedral : 5.878 89.087 2032 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.92 % Allowed : 21.52 % Favored : 75.56 % 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: 2.46 (0.19), residues: 1888 helix: 2.13 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 344 HIS 0.001 0.000 HIS A 328 PHE 0.011 0.001 PHE D 240 TYR 0.010 0.001 TYR A 74 ARG 0.004 0.000 ARG H 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 204 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6857 (mm-30) cc_final: 0.5679 (tt0) REVERT: D 140 GLU cc_start: 0.6834 (mm-30) cc_final: 0.5627 (tt0) REVERT: E 75 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7533 (tpp80) REVERT: F 49 LEU cc_start: 0.8475 (mt) cc_final: 0.8141 (mt) REVERT: F 146 MET cc_start: 0.8635 (tmm) cc_final: 0.7984 (tmm) REVERT: G 52 MET cc_start: 0.7553 (mtt) cc_final: 0.7295 (mtt) REVERT: G 146 MET cc_start: 0.8628 (tmm) cc_final: 0.7980 (tmm) REVERT: H 49 LEU cc_start: 0.8465 (mt) cc_final: 0.8128 (mt) REVERT: H 75 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7539 (tpp80) outliers start: 47 outliers final: 38 residues processed: 238 average time/residue: 0.7324 time to fit residues: 249.0018 Evaluate side-chains 236 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15664 Z= 0.274 Angle : 0.685 14.890 21084 Z= 0.333 Chirality : 0.032 0.142 2336 Planarity : 0.003 0.033 2664 Dihedral : 5.800 86.171 2032 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.17 % Allowed : 21.33 % Favored : 75.50 % 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: 2.27 (0.19), residues: 1888 helix: 1.98 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.50 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 344 HIS 0.002 0.001 HIS B 260 PHE 0.011 0.001 PHE B 548 TYR 0.014 0.001 TYR B 74 ARG 0.004 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 207 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6668 (mm-30) cc_final: 0.5542 (tt0) REVERT: D 140 GLU cc_start: 0.6592 (mm-30) cc_final: 0.5472 (tt0) REVERT: F 146 MET cc_start: 0.8647 (tmm) cc_final: 0.8321 (tmm) REVERT: G 146 MET cc_start: 0.8638 (tmm) cc_final: 0.8315 (tmm) outliers start: 51 outliers final: 45 residues processed: 243 average time/residue: 0.6599 time to fit residues: 229.3341 Evaluate side-chains 239 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15664 Z= 0.228 Angle : 0.675 14.848 21084 Z= 0.321 Chirality : 0.031 0.132 2336 Planarity : 0.003 0.035 2664 Dihedral : 5.719 83.890 2032 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.30 % Allowed : 21.46 % Favored : 75.25 % 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: 2.35 (0.19), residues: 1888 helix: 2.04 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 344 HIS 0.001 0.001 HIS A 260 PHE 0.011 0.001 PHE C 240 TYR 0.011 0.001 TYR A 74 ARG 0.004 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 201 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6624 (mm-30) cc_final: 0.5414 (tt0) REVERT: D 140 GLU cc_start: 0.6616 (mm-30) cc_final: 0.5429 (tt0) REVERT: E 75 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7494 (tpp80) REVERT: F 146 MET cc_start: 0.8657 (tmm) cc_final: 0.8347 (tmm) REVERT: G 146 MET cc_start: 0.8655 (tmm) cc_final: 0.8347 (tmm) REVERT: H 75 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7477 (tpp80) outliers start: 53 outliers final: 49 residues processed: 241 average time/residue: 0.6609 time to fit residues: 226.3267 Evaluate side-chains 245 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 187 optimal weight: 0.0980 chunk 172 optimal weight: 6.9990 chunk 149 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 158 optimal weight: 8.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15664 Z= 0.184 Angle : 0.666 15.176 21084 Z= 0.307 Chirality : 0.031 0.117 2336 Planarity : 0.003 0.032 2664 Dihedral : 5.522 79.599 2032 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.99 % Allowed : 22.76 % Favored : 75.25 % 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: 2.66 (0.19), residues: 1888 helix: 2.23 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 344 HIS 0.001 0.000 HIS C 228 PHE 0.013 0.001 PHE A 240 TYR 0.011 0.001 TYR F 100 ARG 0.005 0.000 ARG E 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6668 (mm-30) cc_final: 0.5598 (tt0) REVERT: D 140 GLU cc_start: 0.6702 (mm-30) cc_final: 0.5624 (tt0) REVERT: E 75 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7589 (tpp80) REVERT: F 146 MET cc_start: 0.8666 (tmm) cc_final: 0.8326 (tmm) REVERT: G 146 MET cc_start: 0.8653 (tmm) cc_final: 0.8313 (tmm) REVERT: H 75 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7564 (tpp80) outliers start: 32 outliers final: 28 residues processed: 230 average time/residue: 0.7498 time to fit residues: 244.6456 Evaluate side-chains 224 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094983 restraints weight = 107335.534| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.87 r_work: 0.3437 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15664 Z= 0.225 Angle : 0.680 14.869 21084 Z= 0.321 Chirality : 0.031 0.132 2336 Planarity : 0.003 0.033 2664 Dihedral : 5.482 79.098 2032 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.24 % Allowed : 23.32 % Favored : 74.44 % 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: 2.60 (0.19), residues: 1888 helix: 2.19 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.27 (0.37), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 344 HIS 0.001 0.001 HIS D 260 PHE 0.014 0.001 PHE C 548 TYR 0.011 0.001 TYR C 74 ARG 0.006 0.000 ARG G 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6193.64 seconds wall clock time: 116 minutes 18.07 seconds (6978.07 seconds total)