Starting phenix.real_space_refine on Fri Mar 22 05:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j01_35880/03_2024/8j01_35880_neut_trim_updated.pdb" } resolution = 3.1 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 P 12 5.49 5 S 88 5.16 5 C 10548 2.51 5 N 2684 2.21 5 O 2900 1.98 5 H 15620 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 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 79": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31852 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} 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: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} 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: 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: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} 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: "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: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} 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: "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: "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: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.49, per 1000 atoms: 0.42 Number of scatterers: 31852 At special positions: 0 Unit cell: (119.97, 120.9, 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 P 12 15.00 O 2900 8.00 N 2684 7.00 C 10548 6.00 H 15620 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 26.18 Conformation dependent library (CDL) restraints added in 3.1 seconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 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 147 removed outlier: 3.844A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.577A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (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 253 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: 4.362A 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 357 through 366 removed outlier: 4.465A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 558 Processing helix chain 'A' and resid 564 through 599 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 147 removed outlier: 3.838A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.639A pdb=" N ARG B 165 " --> pdb=" O LEU B 161 " (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 253 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: 4.322A 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 357 through 366 removed outlier: 4.392A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 558 Processing helix chain 'B' and resid 564 through 599 removed outlier: 3.502A 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 7 through 20 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 139 through 147 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 147 removed outlier: 3.863A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 removed outlier: 3.627A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (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: 4.213A 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 357 through 366 removed outlier: 4.347A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 363 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 558 Processing helix chain 'D' and resid 564 through 599 removed outlier: 3.501A pdb=" N GLY D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Proline residue: D 597 - end of helix 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 74 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 110 Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 91 through 114 Processing helix chain 'G' and resid 119 through 147 removed outlier: 3.863A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 165 removed outlier: 3.604A pdb=" N ARG G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 229 through 254 Processing helix chain 'G' and resid 259 through 261 No H-bonds generated for 'chain 'G' and resid 259 through 261' Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 288 through 348 removed outlier: 4.227A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) Proline residue: G 308 - end of helix Proline residue: G 335 - end of helix Processing helix chain 'G' and resid 357 through 366 removed outlier: 4.307A pdb=" N TYR G 362 " --> pdb=" O SER G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 558 Processing helix chain 'G' and resid 564 through 599 Proline residue: G 597 - end of helix 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 110 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 147 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 110 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 147 1104 hydrogen bonds defined for protein. 3312 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: 11.32 Time building geometry restraints manager: 27.08 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: 15592 1.03 - 1.23: 84 1.23 - 1.43: 6976 1.43 - 1.62: 9360 1.62 - 1.82: 180 Bond restraints: 32192 Sorted by residual: bond pdb=" C07 P0T B 803 " pdb=" C09 P0T B 803 " ideal model delta sigma weight residual 1.336 1.600 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C07 P0T G 802 " pdb=" C09 P0T G 802 " ideal model delta sigma weight residual 1.336 1.598 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C07 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sigma weight residual 1.336 1.598 -0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C07 P0T A 802 " pdb=" C09 P0T A 802 " ideal model delta sigma weight residual 1.336 1.597 -0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C07 P0T G 801 " pdb=" C09 P0T G 801 " ideal model delta sigma weight residual 1.336 1.595 -0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 32187 not shown) Histogram of bond angle deviations from ideal: 81.93 - 92.34: 8 92.34 - 102.76: 68 102.76 - 113.17: 36805 113.17 - 123.59: 18270 123.59 - 134.00: 2645 Bond angle restraints: 57796 Sorted by residual: angle pdb=" C07 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C08 P0T A 801 " ideal model delta sigma weight residual 112.03 81.93 30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C07 P0T D 801 " pdb=" C04 P0T D 801 " pdb=" C08 P0T D 801 " ideal model delta sigma weight residual 112.03 81.98 30.05 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C07 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C08 P0T B 802 " ideal model delta sigma weight residual 112.03 82.02 30.01 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C07 P0T G 801 " pdb=" C04 P0T G 801 " pdb=" C08 P0T G 801 " ideal model delta sigma weight residual 112.03 82.36 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" C07 P0T A 802 " pdb=" C04 P0T A 802 " pdb=" C08 P0T A 802 " ideal model delta sigma weight residual 112.03 83.68 28.35 3.00e+00 1.11e-01 8.93e+01 ... (remaining 57791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 13635 23.04 - 46.07: 1070 46.07 - 69.11: 307 69.11 - 92.15: 42 92.15 - 115.19: 30 Dihedral angle restraints: 15084 sinusoidal: 8144 harmonic: 6940 Sorted by residual: dihedral pdb=" C3 PIO A 803 " pdb=" C1 PIO A 803 " pdb=" C2 PIO A 803 " pdb=" C6 PIO A 803 " ideal model delta sinusoidal sigma weight residual 52.95 -62.24 115.19 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 PIO G 803 " pdb=" C1 PIO G 803 " pdb=" C2 PIO G 803 " pdb=" C6 PIO G 803 " ideal model delta sinusoidal sigma weight residual 52.95 -62.12 115.07 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 PIO D 803 " pdb=" C1 PIO D 803 " pdb=" C2 PIO D 803 " pdb=" C6 PIO D 803 " ideal model delta sinusoidal sigma weight residual 52.95 -61.99 114.94 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 15081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1663 0.025 - 0.050: 519 0.050 - 0.074: 195 0.074 - 0.099: 72 0.099 - 0.124: 23 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CA PRO H 67 " pdb=" N PRO H 67 " pdb=" C PRO H 67 " pdb=" CB PRO H 67 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.83e-01 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 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CB THR F 35 " pdb=" CA THR F 35 " pdb=" OG1 THR F 35 " pdb=" CG2 THR F 35 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 2469 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO H 67 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 87 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO G 88 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 88 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 88 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 87 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 88 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " -0.016 5.00e-02 4.00e+02 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1256 2.14 - 2.76: 59536 2.76 - 3.37: 95247 3.37 - 3.99: 112365 3.99 - 4.60: 179310 Nonbonded interactions: 447714 Sorted by model distance: nonbonded pdb=" O ILE C 53 " pdb=" H ASP C 57 " model vdw 1.525 1.850 nonbonded pdb="HH21 ARG D 332 " pdb=" O ARG D 560 " model vdw 1.526 1.850 nonbonded pdb="HH21 ARG A 332 " pdb=" O ARG A 560 " model vdw 1.547 1.850 nonbonded pdb=" O ILE E 53 " pdb=" H ASP E 57 " model vdw 1.557 1.850 nonbonded pdb=" O ILE F 53 " pdb=" H ASP F 57 " model vdw 1.561 1.850 ... (remaining 447709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 600 or resid 802)) selection = (chain 'B' and (resid 70 through 600 or resid 802)) selection = (chain 'D' and (resid 70 through 600 or resid 802)) selection = (chain 'G' and (resid 70 through 600 or resid 802)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 4.850 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 98.110 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.011 0.264 16572 Z= 0.699 Angle : 0.927 30.102 22324 Z= 0.384 Chirality : 0.031 0.124 2472 Planarity : 0.003 0.032 2780 Dihedral : 19.636 115.185 6120 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.60 % Allowed : 21.30 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.19), residues: 1956 helix: 1.90 (0.13), residues: 1580 sheet: None (None), residues: 0 loop : 0.24 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.002 0.001 HIS D 260 PHE 0.009 0.001 PHE B 168 TYR 0.010 0.001 TYR C 139 ARG 0.002 0.000 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 231 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 221 time to evaluate : 2.459 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: B 146 TRP cc_start: 0.5635 (t60) cc_final: 0.5358 (t60) REVERT: B 155 ARG cc_start: 0.5217 (mmt180) cc_final: 0.4591 (mmm160) REVERT: B 158 ARG cc_start: 0.4941 (mtt180) cc_final: 0.4492 (tpt170) REVERT: C 40 LEU cc_start: 0.8601 (mm) cc_final: 0.8275 (tp) REVERT: D 158 ARG cc_start: 0.4911 (mtt180) cc_final: 0.4291 (tpt170) REVERT: F 52 MET cc_start: 0.7564 (ttm) cc_final: 0.7048 (ttm) outliers start: 10 outliers final: 8 residues processed: 221 average time/residue: 0.6731 time to fit residues: 214.0862 Evaluate side-chains 187 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 571 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7618 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16572 Z= 0.180 Angle : 0.554 9.662 22324 Z= 0.276 Chirality : 0.032 0.133 2472 Planarity : 0.003 0.032 2780 Dihedral : 12.425 99.132 2412 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.91 % Allowed : 20.11 % Favored : 77.98 % 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: 2.49 (0.19), residues: 1956 helix: 2.05 (0.13), residues: 1564 sheet: None (None), residues: 0 loop : 0.08 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.002 0.001 HIS A 228 PHE 0.012 0.001 PHE B 168 TYR 0.009 0.001 TYR C 139 ARG 0.005 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 217 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 2.025 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: B 155 ARG cc_start: 0.5196 (mmt180) cc_final: 0.4524 (mmm160) REVERT: B 158 ARG cc_start: 0.4953 (mtt180) cc_final: 0.4499 (tpt170) REVERT: C 40 LEU cc_start: 0.8542 (mm) cc_final: 0.8257 (tp) REVERT: C 110 MET cc_start: 0.8747 (mmm) cc_final: 0.8286 (mmp) REVERT: D 158 ARG cc_start: 0.4921 (mtt180) cc_final: 0.4263 (tpt170) REVERT: H 51 ASP cc_start: 0.8145 (t0) cc_final: 0.7728 (m-30) outliers start: 32 outliers final: 21 residues processed: 198 average time/residue: 0.6587 time to fit residues: 191.6525 Evaluate side-chains 190 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16572 Z= 0.243 Angle : 0.515 7.379 22324 Z= 0.275 Chirality : 0.032 0.128 2472 Planarity : 0.003 0.032 2780 Dihedral : 9.467 92.290 2406 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 20.94 % Favored : 76.73 % 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: 2.39 (0.19), residues: 1956 helix: 1.99 (0.13), residues: 1564 sheet: None (None), residues: 0 loop : 0.01 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.002 0.001 HIS D 96 PHE 0.009 0.001 PHE B 168 TYR 0.009 0.001 TYR C 139 ARG 0.006 0.000 ARG G 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 211 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 172 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ARG cc_start: 0.5031 (mmt180) cc_final: 0.4384 (mmm160) REVERT: B 158 ARG cc_start: 0.5036 (mtt180) cc_final: 0.4573 (tpt170) REVERT: C 110 MET cc_start: 0.8772 (mmm) cc_final: 0.8360 (mmp) REVERT: D 158 ARG cc_start: 0.4943 (mtt180) cc_final: 0.4272 (tpt170) REVERT: F 144 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8623 (tm-30) REVERT: G 158 ARG cc_start: 0.4883 (mtt180) cc_final: 0.4213 (tpt170) REVERT: H 51 ASP cc_start: 0.8264 (t0) cc_final: 0.7840 (m-30) REVERT: H 110 MET cc_start: 0.8903 (mmm) cc_final: 0.8482 (mmp) outliers start: 39 outliers final: 31 residues processed: 192 average time/residue: 0.7279 time to fit residues: 205.0038 Evaluate side-chains 198 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN H 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16572 Z= 0.284 Angle : 0.534 7.543 22324 Z= 0.288 Chirality : 0.033 0.130 2472 Planarity : 0.003 0.040 2780 Dihedral : 9.328 89.747 2406 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.74 % Allowed : 21.00 % Favored : 76.25 % 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: 2.23 (0.19), residues: 1956 helix: 1.88 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.04 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 344 HIS 0.002 0.001 HIS G 96 PHE 0.010 0.001 PHE B 137 TYR 0.010 0.001 TYR A 562 ARG 0.004 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 221 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5035 (mtt180) cc_final: 0.4540 (tpt170) REVERT: B 131 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7403 (tp) REVERT: B 155 ARG cc_start: 0.5053 (mmt180) cc_final: 0.4344 (mmm160) REVERT: B 158 ARG cc_start: 0.5007 (mtt180) cc_final: 0.4552 (tpt170) REVERT: C 110 MET cc_start: 0.8804 (mmm) cc_final: 0.8458 (mmp) REVERT: D 158 ARG cc_start: 0.4943 (mtt180) cc_final: 0.4283 (tpt170) REVERT: F 144 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8640 (tm-30) REVERT: G 158 ARG cc_start: 0.4852 (mtt180) cc_final: 0.4178 (tpt170) REVERT: H 51 ASP cc_start: 0.8386 (t0) cc_final: 0.8046 (m-30) REVERT: H 110 MET cc_start: 0.9031 (mmm) cc_final: 0.8725 (mmp) outliers start: 46 outliers final: 34 residues processed: 202 average time/residue: 0.7066 time to fit residues: 202.6452 Evaluate side-chains 203 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.7682 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16572 Z= 0.310 Angle : 0.549 8.119 22324 Z= 0.297 Chirality : 0.034 0.131 2472 Planarity : 0.004 0.035 2780 Dihedral : 9.303 89.913 2404 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.76 % Allowed : 20.64 % Favored : 75.60 % 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: 2.04 (0.19), residues: 1956 helix: 1.74 (0.12), residues: 1564 sheet: None (None), residues: 0 loop : -0.06 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 344 HIS 0.002 0.001 HIS D 96 PHE 0.011 0.001 PHE B 137 TYR 0.010 0.001 TYR B 562 ARG 0.003 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 245 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5155 (mtt180) cc_final: 0.4635 (tpt170) REVERT: B 131 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7459 (tp) REVERT: B 158 ARG cc_start: 0.5122 (mtt180) cc_final: 0.4639 (tpt170) REVERT: C 110 MET cc_start: 0.8769 (mmm) cc_final: 0.8475 (mmp) REVERT: D 130 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6858 (tm-30) REVERT: D 131 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7464 (tp) REVERT: D 158 ARG cc_start: 0.4937 (mtt180) cc_final: 0.4281 (tpt170) REVERT: G 78 GLN cc_start: 0.4805 (OUTLIER) cc_final: 0.4359 (tt0) REVERT: G 131 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7445 (tp) REVERT: G 158 ARG cc_start: 0.4810 (mtt180) cc_final: 0.4161 (tpt170) REVERT: H 51 ASP cc_start: 0.8396 (t0) cc_final: 0.8100 (m-30) REVERT: H 110 MET cc_start: 0.9029 (mmm) cc_final: 0.8795 (mmp) REVERT: E 110 MET cc_start: 0.8806 (mmm) cc_final: 0.8412 (mmp) outliers start: 63 outliers final: 43 residues processed: 220 average time/residue: 0.7096 time to fit residues: 221.5989 Evaluate side-chains 217 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 170 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 78 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16572 Z= 0.260 Angle : 0.545 8.190 22324 Z= 0.290 Chirality : 0.033 0.174 2472 Planarity : 0.006 0.169 2780 Dihedral : 9.101 89.317 2404 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.28 % Allowed : 21.18 % Favored : 75.54 % 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: 2.10 (0.19), residues: 1956 helix: 1.81 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -0.16 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.003 0.001 HIS D 96 PHE 0.010 0.001 PHE A 168 TYR 0.009 0.001 TYR B 562 ARG 0.016 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 236 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 181 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5141 (mtt180) cc_final: 0.4618 (tpt170) REVERT: B 158 ARG cc_start: 0.5107 (mtt180) cc_final: 0.4624 (tpt170) REVERT: D 155 ARG cc_start: 0.5146 (mmt180) cc_final: 0.4384 (mmm160) REVERT: D 158 ARG cc_start: 0.4901 (mtt180) cc_final: 0.4245 (tpt170) REVERT: D 578 MET cc_start: 0.8590 (ttm) cc_final: 0.8387 (ttm) REVERT: G 158 ARG cc_start: 0.4777 (mtt180) cc_final: 0.4132 (tpt170) REVERT: H 51 ASP cc_start: 0.8480 (t0) cc_final: 0.8109 (m-30) REVERT: E 110 MET cc_start: 0.8770 (mmm) cc_final: 0.8495 (mmp) outliers start: 55 outliers final: 46 residues processed: 214 average time/residue: 0.6795 time to fit residues: 209.2086 Evaluate side-chains 222 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 HIS G 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16572 Z= 0.217 Angle : 0.522 8.750 22324 Z= 0.278 Chirality : 0.033 0.214 2472 Planarity : 0.004 0.093 2780 Dihedral : 8.715 87.433 2404 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.92 % Allowed : 22.02 % Favored : 75.06 % 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: 2.21 (0.19), residues: 1956 helix: 1.89 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.17 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.005 0.001 HIS D 96 PHE 0.012 0.001 PHE F 66 TYR 0.009 0.001 TYR C 139 ARG 0.012 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 233 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5119 (mtt180) cc_final: 0.4608 (tpt170) REVERT: B 158 ARG cc_start: 0.5100 (mtt180) cc_final: 0.4624 (tpt170) REVERT: C 144 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8662 (tm-30) REVERT: D 158 ARG cc_start: 0.4896 (mtt180) cc_final: 0.4240 (tpt170) REVERT: G 78 GLN cc_start: 0.4889 (OUTLIER) cc_final: 0.4481 (tt0) REVERT: G 158 ARG cc_start: 0.4771 (mtt180) cc_final: 0.4127 (tpt170) REVERT: H 51 ASP cc_start: 0.8497 (t0) cc_final: 0.8144 (m-30) REVERT: E 110 MET cc_start: 0.8745 (mmm) cc_final: 0.8440 (mmp) outliers start: 49 outliers final: 41 residues processed: 215 average time/residue: 0.7539 time to fit residues: 234.5275 Evaluate side-chains 213 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain G residue 78 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 93 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16572 Z= 0.191 Angle : 0.513 8.779 22324 Z= 0.272 Chirality : 0.032 0.165 2472 Planarity : 0.004 0.107 2780 Dihedral : 8.479 86.018 2402 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.63 % Allowed : 22.73 % Favored : 74.64 % 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: 2.34 (0.19), residues: 1956 helix: 1.98 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.11 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.002 0.000 HIS A 575 PHE 0.010 0.001 PHE F 66 TYR 0.009 0.001 TYR C 139 ARG 0.007 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 228 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5114 (mtt180) cc_final: 0.4604 (tpt170) REVERT: B 158 ARG cc_start: 0.5064 (mtt180) cc_final: 0.4598 (tpt170) REVERT: C 78 LYS cc_start: 0.8367 (mtmm) cc_final: 0.8041 (mttt) REVERT: C 144 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8641 (tm-30) REVERT: D 158 ARG cc_start: 0.4814 (mtt180) cc_final: 0.4180 (tpt170) REVERT: G 155 ARG cc_start: 0.5410 (mmt180) cc_final: 0.4686 (mmm160) REVERT: G 158 ARG cc_start: 0.4772 (mtt180) cc_final: 0.4125 (tpt170) REVERT: H 51 ASP cc_start: 0.8484 (t0) cc_final: 0.8136 (m-30) REVERT: E 110 MET cc_start: 0.8718 (mmm) cc_final: 0.8425 (mmp) outliers start: 44 outliers final: 38 residues processed: 209 average time/residue: 0.6689 time to fit residues: 200.1061 Evaluate side-chains 217 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 179 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16572 Z= 0.217 Angle : 0.520 9.134 22324 Z= 0.277 Chirality : 0.032 0.146 2472 Planarity : 0.004 0.094 2780 Dihedral : 8.646 87.104 2402 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.86 % Allowed : 22.73 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.19), residues: 1956 helix: 1.96 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.13 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.002 0.000 HIS A 575 PHE 0.010 0.001 PHE F 66 TYR 0.010 0.001 TYR B 363 ARG 0.007 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 230 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5150 (mtt180) cc_final: 0.4629 (tpt170) REVERT: B 158 ARG cc_start: 0.5079 (mtt180) cc_final: 0.4603 (tpt170) REVERT: C 144 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8630 (tm-30) REVERT: D 158 ARG cc_start: 0.4830 (mtt180) cc_final: 0.4183 (tpt170) REVERT: G 155 ARG cc_start: 0.5370 (mmt180) cc_final: 0.4644 (mmm160) REVERT: G 158 ARG cc_start: 0.4787 (mtt180) cc_final: 0.4129 (tpt170) REVERT: H 51 ASP cc_start: 0.8510 (t0) cc_final: 0.8148 (m-30) REVERT: E 110 MET cc_start: 0.8734 (mmm) cc_final: 0.8461 (mmp) outliers start: 48 outliers final: 42 residues processed: 211 average time/residue: 0.6828 time to fit residues: 207.0367 Evaluate side-chains 214 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16572 Z= 0.231 Angle : 0.533 9.423 22324 Z= 0.283 Chirality : 0.033 0.160 2472 Planarity : 0.004 0.075 2780 Dihedral : 8.562 87.757 2402 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.68 % Allowed : 23.09 % Favored : 74.22 % 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: 2.28 (0.19), residues: 1956 helix: 1.95 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.002 0.000 HIS A 575 PHE 0.010 0.001 PHE D 168 TYR 0.009 0.001 TYR C 139 ARG 0.007 0.000 ARG G 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 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 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 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 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 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 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 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. Evaluate side-chains 219 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5158 (mtt180) cc_final: 0.4633 (tpt170) REVERT: B 158 ARG cc_start: 0.5080 (mtt180) cc_final: 0.4600 (tpt170) REVERT: C 144 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8629 (tm-30) REVERT: D 158 ARG cc_start: 0.4817 (mtt180) cc_final: 0.4179 (tpt170) REVERT: G 155 ARG cc_start: 0.5377 (mmt180) cc_final: 0.4649 (mmm160) REVERT: G 158 ARG cc_start: 0.4813 (mtt180) cc_final: 0.4134 (tpt170) REVERT: H 51 ASP cc_start: 0.8503 (t0) cc_final: 0.8129 (m-30) REVERT: E 110 MET cc_start: 0.8761 (mmm) cc_final: 0.8487 (mmp) outliers start: 45 outliers final: 45 residues processed: 203 average time/residue: 0.7000 time to fit residues: 203.5279 Evaluate side-chains 216 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.158462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.107220 restraints weight = 77969.075| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.98 r_work: 0.3260 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 16572 Z= 0.269 Angle : 0.889 59.200 22324 Z= 0.455 Chirality : 0.033 0.251 2472 Planarity : 0.007 0.255 2780 Dihedral : 8.474 87.753 2402 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.68 % Allowed : 23.03 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 1956 helix: 1.95 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.002 0.000 HIS A 575 PHE 0.011 0.001 PHE F 66 TYR 0.009 0.001 TYR C 139 ARG 0.074 0.001 ARG D 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6848.99 seconds wall clock time: 121 minutes 37.84 seconds (7297.84 seconds total)