Starting phenix.real_space_refine on Sat Aug 10 19:20:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/08_2024/8x43_38041_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/08_2024/8x43_38041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/08_2024/8x43_38041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/08_2024/8x43_38041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/08_2024/8x43_38041_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x43_38041/08_2024/8x43_38041_neut_trim.cif" } resolution = 3.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 88 5.16 5 C 9804 2.51 5 N 2572 2.21 5 O 2712 1.98 5 F 4 1.80 5 H 14984 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 566": "OD1" <-> "OD2" Residue "C ASP 577": "OD1" <-> "OD2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 566": "OD1" <-> "OD2" Residue "E ASP 577": "OD1" <-> "OD2" Residue "E ASP 590": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G ASP 566": "OD1" <-> "OD2" Residue "G ASP 577": "OD1" <-> "OD2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30164 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" 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: "C" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" 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: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 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: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.00, per 1000 atoms: 0.46 Number of scatterers: 30164 At special positions: 0 Unit cell: (125.55, 125.55, 120.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 F 4 9.00 O 2712 8.00 N 2572 7.00 C 9804 6.00 H 14984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.02 Conformation dependent library (CDL) restraints added in 2.9 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 4 sheets defined 83.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 3.896A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.016A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 166 through 182 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 330 removed outlier: 4.165A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.055A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.645A pdb=" N ALA A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 560 Processing helix chain 'A' and resid 563 through 595 removed outlier: 4.034A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 21 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.838A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.748A pdb=" N VAL B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 115 removed outlier: 3.897A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 4.015A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 155 through 165 Processing helix chain 'C' and resid 166 through 182 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 330 removed outlier: 4.165A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix removed outlier: 4.071A pdb=" N HIS C 328 " --> pdb=" O HIS C 324 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE C 329 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 350 removed outlier: 3.683A pdb=" N ALA C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 560 Processing helix chain 'C' and resid 563 through 595 removed outlier: 3.953A pdb=" N VAL C 567 " --> pdb=" O ASP C 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.751A pdb=" N VAL D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'E' and resid 71 through 86 Processing helix chain 'E' and resid 91 through 115 removed outlier: 3.895A pdb=" N TYR E 95 " --> pdb=" O TRP E 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 148 removed outlier: 4.018A pdb=" N ILE E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 155 through 165 Processing helix chain 'E' and resid 166 through 182 Processing helix chain 'E' and resid 196 through 211 Processing helix chain 'E' and resid 215 through 228 Processing helix chain 'E' and resid 228 through 255 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 287 through 327 removed outlier: 4.168A pdb=" N ILE E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) Proline residue: E 308 - end of helix Processing helix chain 'E' and resid 332 through 350 removed outlier: 3.736A pdb=" N ALA E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN E 350 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 560 Processing helix chain 'E' and resid 563 through 595 removed outlier: 4.064A pdb=" N VAL E 567 " --> pdb=" O ASP E 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.704A pdb=" N VAL F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 148 Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 115 removed outlier: 3.900A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 4.033A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 166 through 182 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 255 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 330 removed outlier: 4.168A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix removed outlier: 4.055A pdb=" N HIS G 328 " --> pdb=" O HIS G 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE G 329 " --> pdb=" O ARG G 325 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU G 330 " --> pdb=" O GLN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 350 removed outlier: 3.676A pdb=" N ALA G 336 " --> pdb=" O ARG G 332 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 560 Processing helix chain 'G' and resid 563 through 595 removed outlier: 3.965A pdb=" N VAL G 567 " --> pdb=" O ASP G 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.854A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 102 through 113 removed outlier: 3.543A pdb=" N LEU H 113 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.640A pdb=" N VAL H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 101 1170 hydrogen bonds defined for protein. 3498 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: 12.10 Time building geometry restraints manager: 27.21 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: 14956 1.03 - 1.23: 39 1.23 - 1.42: 6685 1.42 - 1.62: 8660 1.62 - 1.81: 148 Bond restraints: 30488 Sorted by residual: bond pdb=" C13 7Q0 C 801 " pdb=" N1 7Q0 C 801 " ideal model delta sigma weight residual 1.354 1.443 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C13 7Q0 E 801 " pdb=" N1 7Q0 E 801 " ideal model delta sigma weight residual 1.354 1.442 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C13 7Q0 G 801 " pdb=" N1 7Q0 G 801 " ideal model delta sigma weight residual 1.354 1.442 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C13 7Q0 A 801 " pdb=" N1 7Q0 A 801 " ideal model delta sigma weight residual 1.354 1.442 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C8 7Q0 A 801 " pdb=" N2 7Q0 A 801 " ideal model delta sigma weight residual 1.370 1.447 -0.077 2.00e-02 2.50e+03 1.46e+01 ... (remaining 30483 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 272 106.51 - 113.38: 34712 113.38 - 120.26: 11267 120.26 - 127.13: 8446 127.13 - 134.01: 139 Bond angle restraints: 54836 Sorted by residual: angle pdb=" CB MET D 125 " pdb=" CG MET D 125 " pdb=" SD MET D 125 " ideal model delta sigma weight residual 112.70 119.54 -6.84 3.00e+00 1.11e-01 5.20e+00 angle pdb=" CB MET B 125 " pdb=" CG MET B 125 " pdb=" SD MET B 125 " ideal model delta sigma weight residual 112.70 119.49 -6.79 3.00e+00 1.11e-01 5.12e+00 angle pdb=" CB MET H 125 " pdb=" CG MET H 125 " pdb=" SD MET H 125 " ideal model delta sigma weight residual 112.70 119.45 -6.75 3.00e+00 1.11e-01 5.06e+00 angle pdb=" N ARG C 213 " pdb=" CA ARG C 213 " pdb=" CB ARG C 213 " ideal model delta sigma weight residual 113.65 110.47 3.18 1.47e+00 4.63e-01 4.68e+00 angle pdb=" N ARG G 213 " pdb=" CA ARG G 213 " pdb=" CB ARG G 213 " ideal model delta sigma weight residual 113.65 110.48 3.17 1.47e+00 4.63e-01 4.66e+00 ... (remaining 54831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12358 17.90 - 35.81: 1303 35.81 - 53.71: 402 53.71 - 71.61: 91 71.61 - 89.52: 18 Dihedral angle restraints: 14172 sinusoidal: 7544 harmonic: 6628 Sorted by residual: dihedral pdb=" CA THR B 111 " pdb=" C THR B 111 " pdb=" N ASN B 112 " pdb=" CA ASN B 112 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR D 111 " pdb=" C THR D 111 " pdb=" N ASN D 112 " pdb=" CA ASN D 112 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR F 111 " pdb=" C THR F 111 " pdb=" N ASN F 112 " pdb=" CA ASN F 112 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1629 0.032 - 0.064: 491 0.064 - 0.096: 138 0.096 - 0.129: 29 0.129 - 0.161: 1 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA ILE F 101 " pdb=" N ILE F 101 " pdb=" C ILE F 101 " pdb=" CB ILE F 101 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR G 296 " pdb=" CA THR G 296 " pdb=" OG1 THR G 296 " pdb=" CG2 THR G 296 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB THR A 296 " pdb=" CA THR A 296 " pdb=" OG1 THR A 296 " pdb=" CG2 THR A 296 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 2285 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 560 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO E 561 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 561 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 561 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 560 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO G 561 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 561 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 561 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR G 298 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C THR G 298 " 0.023 2.00e-02 2.50e+03 pdb=" O THR G 298 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU G 299 " -0.008 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1956 2.18 - 2.79: 61777 2.79 - 3.39: 89225 3.39 - 4.00: 107061 4.00 - 4.60: 168885 Nonbonded interactions: 428904 Sorted by model distance: nonbonded pdb=" O ARG B 91 " pdb="HH11 ARG B 91 " model vdw 1.580 2.450 nonbonded pdb=" O ARG H 91 " pdb="HH11 ARG H 91 " model vdw 1.580 2.450 nonbonded pdb=" HH TYR A 95 " pdb=" OE1 GLU A 140 " model vdw 1.582 2.450 nonbonded pdb=" HH TYR G 95 " pdb=" OE1 GLU G 140 " model vdw 1.585 2.450 nonbonded pdb=" HH TYR E 95 " pdb=" OE1 GLU E 140 " model vdw 1.586 2.450 ... (remaining 428899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' 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: 0.650 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: 0.480 Extract box with map and model: 1.290 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 98.450 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 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:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 15504 Z= 0.313 Angle : 0.564 6.842 20912 Z= 0.313 Chirality : 0.034 0.161 2288 Planarity : 0.003 0.050 2636 Dihedral : 17.005 89.519 5604 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.38 % Allowed : 23.36 % Favored : 76.26 % 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 (0.20), residues: 1848 helix: 2.03 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 91 HIS 0.003 0.001 HIS C 228 PHE 0.017 0.001 PHE C 329 TYR 0.010 0.001 TYR G 74 ARG 0.003 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 315 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6289 (ptp90) cc_final: 0.5819 (ptm-80) REVERT: A 123 GLU cc_start: 0.7050 (tp30) cc_final: 0.6218 (tt0) REVERT: A 322 GLU cc_start: 0.7715 (tp30) cc_final: 0.7082 (mt-10) REVERT: A 334 ASN cc_start: 0.8055 (m-40) cc_final: 0.7818 (m110) REVERT: A 342 SER cc_start: 0.6464 (OUTLIER) cc_final: 0.6033 (m) REVERT: A 553 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7180 (tpt-90) REVERT: A 578 MET cc_start: 0.7306 (ptt) cc_final: 0.6969 (mmm) REVERT: B 73 MET cc_start: -0.1826 (mmm) cc_final: -0.2348 (ttm) REVERT: B 87 ARG cc_start: 0.5032 (tpp80) cc_final: 0.4823 (tmt-80) REVERT: B 106 LEU cc_start: 0.7011 (tp) cc_final: 0.6774 (tm) REVERT: B 107 ARG cc_start: 0.3520 (mtt90) cc_final: 0.3269 (tpp-160) REVERT: B 134 ASP cc_start: 0.5168 (p0) cc_final: 0.4149 (m-30) REVERT: C 89 ARG cc_start: 0.6196 (ptp90) cc_final: 0.5809 (ptm-80) REVERT: C 123 GLU cc_start: 0.7047 (tp30) cc_final: 0.6209 (tt0) REVERT: C 322 GLU cc_start: 0.7743 (tp30) cc_final: 0.7080 (mt-10) REVERT: C 334 ASN cc_start: 0.8006 (m-40) cc_final: 0.7791 (m110) REVERT: C 342 SER cc_start: 0.6421 (OUTLIER) cc_final: 0.5993 (m) REVERT: D 73 MET cc_start: -0.2785 (mmt) cc_final: -0.3313 (ttm) REVERT: D 106 LEU cc_start: 0.6998 (tp) cc_final: 0.6789 (tm) REVERT: D 134 ASP cc_start: 0.5189 (p0) cc_final: 0.4157 (m-30) REVERT: D 142 PHE cc_start: 0.6645 (t80) cc_final: 0.6226 (t80) REVERT: D 146 MET cc_start: 0.6280 (mmm) cc_final: 0.5630 (mmm) REVERT: E 89 ARG cc_start: 0.6189 (ptp90) cc_final: 0.5769 (ptm-80) REVERT: E 123 GLU cc_start: 0.7109 (tp30) cc_final: 0.6259 (tt0) REVERT: E 152 CYS cc_start: 0.7820 (m) cc_final: 0.7378 (t) REVERT: E 322 GLU cc_start: 0.7714 (tp30) cc_final: 0.7055 (mt-10) REVERT: E 334 ASN cc_start: 0.8013 (m-40) cc_final: 0.7755 (m110) REVERT: E 342 SER cc_start: 0.6372 (OUTLIER) cc_final: 0.5950 (m) REVERT: F 72 MET cc_start: -0.0260 (ptt) cc_final: -0.0462 (tmm) REVERT: F 73 MET cc_start: -0.1943 (mmm) cc_final: -0.2449 (ttm) REVERT: F 134 ASP cc_start: 0.5021 (p0) cc_final: 0.4004 (m-30) REVERT: F 142 PHE cc_start: 0.6706 (t80) cc_final: 0.6361 (t80) REVERT: F 146 MET cc_start: 0.6143 (mmm) cc_final: 0.5492 (mmm) REVERT: G 89 ARG cc_start: 0.6246 (ptp90) cc_final: 0.5681 (ptm-80) REVERT: G 123 GLU cc_start: 0.7091 (tp30) cc_final: 0.6250 (tt0) REVERT: G 152 CYS cc_start: 0.7893 (m) cc_final: 0.7408 (t) REVERT: G 322 GLU cc_start: 0.7697 (tp30) cc_final: 0.7226 (mt-10) REVERT: G 334 ASN cc_start: 0.7985 (m-40) cc_final: 0.7698 (m110) REVERT: G 342 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5947 (m) REVERT: G 553 ARG cc_start: 0.7587 (mpt180) cc_final: 0.7037 (tpp80) REVERT: G 578 MET cc_start: 0.6921 (ptt) cc_final: 0.6586 (mmm) REVERT: H 72 MET cc_start: -0.0290 (ptt) cc_final: -0.0716 (tmm) REVERT: H 73 MET cc_start: -0.1817 (tpt) cc_final: -0.2833 (ttm) REVERT: H 87 ARG cc_start: 0.5257 (tpp80) cc_final: 0.4957 (tmt-80) REVERT: H 134 ASP cc_start: 0.5129 (p0) cc_final: 0.4089 (m-30) REVERT: H 142 PHE cc_start: 0.6759 (t80) cc_final: 0.6537 (t80) outliers start: 6 outliers final: 4 residues processed: 314 average time/residue: 2.6262 time to fit residues: 910.7513 Evaluate side-chains 255 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15504 Z= 0.306 Angle : 0.537 5.360 20912 Z= 0.293 Chirality : 0.035 0.136 2288 Planarity : 0.004 0.034 2636 Dihedral : 4.478 51.228 2084 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.53 % Allowed : 22.54 % Favored : 74.94 % 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: 2.14 (0.19), residues: 1848 helix: 1.99 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.94 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.005 0.001 HIS E 228 PHE 0.015 0.001 PHE E 329 TYR 0.013 0.001 TYR A 74 ARG 0.003 0.000 ARG G 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 286 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 246 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6295 (ptp90) cc_final: 0.5837 (ptm-80) REVERT: A 123 GLU cc_start: 0.6786 (tp30) cc_final: 0.6147 (tt0) REVERT: A 322 GLU cc_start: 0.7566 (tp30) cc_final: 0.7180 (mt-10) REVERT: A 334 ASN cc_start: 0.7875 (m-40) cc_final: 0.7617 (m110) REVERT: A 342 SER cc_start: 0.6171 (OUTLIER) cc_final: 0.5615 (m) REVERT: A 544 CYS cc_start: 0.5416 (OUTLIER) cc_final: 0.4048 (m) REVERT: A 553 ARG cc_start: 0.7606 (mpt180) cc_final: 0.7024 (tpt-90) REVERT: A 578 MET cc_start: 0.7369 (ptt) cc_final: 0.6862 (mmm) REVERT: B 72 MET cc_start: 0.1638 (tmm) cc_final: 0.1234 (tmm) REVERT: B 77 MET cc_start: 0.1156 (OUTLIER) cc_final: -0.0422 (mtt) REVERT: B 107 ARG cc_start: 0.3487 (mtt90) cc_final: 0.3216 (tpp-160) REVERT: B 134 ASP cc_start: 0.5209 (p0) cc_final: 0.3891 (t0) REVERT: C 89 ARG cc_start: 0.6324 (ptp90) cc_final: 0.5864 (ptm-80) REVERT: C 123 GLU cc_start: 0.6785 (tp30) cc_final: 0.6140 (tt0) REVERT: C 322 GLU cc_start: 0.7505 (tp30) cc_final: 0.7209 (mt-10) REVERT: C 334 ASN cc_start: 0.7877 (m-40) cc_final: 0.7643 (m110) REVERT: C 342 SER cc_start: 0.6252 (OUTLIER) cc_final: 0.5724 (m) REVERT: C 544 CYS cc_start: 0.4753 (OUTLIER) cc_final: 0.3651 (m) REVERT: D 72 MET cc_start: 0.1570 (tmm) cc_final: 0.1296 (tmm) REVERT: D 73 MET cc_start: -0.2770 (mmt) cc_final: -0.3159 (ttm) REVERT: D 134 ASP cc_start: 0.5231 (p0) cc_final: 0.3828 (t0) REVERT: D 142 PHE cc_start: 0.6877 (t80) cc_final: 0.6585 (t80) REVERT: D 146 MET cc_start: 0.6342 (mmm) cc_final: 0.6028 (mmm) REVERT: E 89 ARG cc_start: 0.6318 (ptp90) cc_final: 0.5844 (ptm-80) REVERT: E 123 GLU cc_start: 0.6871 (tp30) cc_final: 0.6226 (tt0) REVERT: E 176 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7146 (mp) REVERT: E 322 GLU cc_start: 0.7538 (tp30) cc_final: 0.7100 (mt-10) REVERT: E 334 ASN cc_start: 0.7951 (m-40) cc_final: 0.7666 (m110) REVERT: E 342 SER cc_start: 0.6078 (OUTLIER) cc_final: 0.5610 (m) REVERT: E 544 CYS cc_start: 0.5092 (OUTLIER) cc_final: 0.3736 (m) REVERT: E 570 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7546 (tm-30) REVERT: F 72 MET cc_start: 0.0055 (ptt) cc_final: -0.0287 (tmm) REVERT: F 73 MET cc_start: -0.2051 (mmm) cc_final: -0.2485 (ttm) REVERT: F 77 MET cc_start: 0.0561 (OUTLIER) cc_final: 0.0181 (mtt) REVERT: F 134 ASP cc_start: 0.5055 (p0) cc_final: 0.3695 (t0) REVERT: F 142 PHE cc_start: 0.6922 (t80) cc_final: 0.6532 (t80) REVERT: F 146 MET cc_start: 0.6437 (mmm) cc_final: 0.5881 (mmm) REVERT: G 89 ARG cc_start: 0.6368 (ptp90) cc_final: 0.5822 (ptm-80) REVERT: G 123 GLU cc_start: 0.6858 (tp30) cc_final: 0.6217 (tt0) REVERT: G 322 GLU cc_start: 0.7754 (tp30) cc_final: 0.7302 (mt-10) REVERT: G 334 ASN cc_start: 0.7906 (m-40) cc_final: 0.7618 (m110) REVERT: G 342 SER cc_start: 0.6279 (OUTLIER) cc_final: 0.5770 (m) REVERT: G 544 CYS cc_start: 0.5167 (OUTLIER) cc_final: 0.3952 (m) REVERT: G 553 ARG cc_start: 0.7662 (mpt180) cc_final: 0.7183 (tpt-90) REVERT: H 72 MET cc_start: -0.0485 (OUTLIER) cc_final: -0.0820 (tmm) REVERT: H 73 MET cc_start: -0.1816 (tpt) cc_final: -0.2810 (ttm) REVERT: H 134 ASP cc_start: 0.5118 (p0) cc_final: 0.3754 (t0) outliers start: 40 outliers final: 8 residues processed: 271 average time/residue: 2.3789 time to fit residues: 718.9398 Evaluate side-chains 246 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15504 Z= 0.313 Angle : 0.528 5.112 20912 Z= 0.286 Chirality : 0.035 0.133 2288 Planarity : 0.004 0.036 2636 Dihedral : 4.413 50.947 2078 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.21 % Allowed : 24.37 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 1848 helix: 1.99 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 91 HIS 0.004 0.001 HIS A 96 PHE 0.016 0.001 PHE E 329 TYR 0.014 0.001 TYR A 74 ARG 0.005 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 257 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6290 (ptp90) cc_final: 0.5808 (ptm-80) REVERT: A 322 GLU cc_start: 0.7556 (tp30) cc_final: 0.7117 (mt-10) REVERT: A 334 ASN cc_start: 0.7911 (m-40) cc_final: 0.7655 (m110) REVERT: A 342 SER cc_start: 0.6150 (OUTLIER) cc_final: 0.5618 (m) REVERT: A 544 CYS cc_start: 0.5233 (OUTLIER) cc_final: 0.3869 (m) REVERT: A 553 ARG cc_start: 0.7587 (mpt180) cc_final: 0.6984 (tpt-90) REVERT: A 578 MET cc_start: 0.7014 (ptt) cc_final: 0.6793 (mmm) REVERT: B 91 ARG cc_start: 0.8413 (ptm160) cc_final: 0.8186 (ptm160) REVERT: B 107 ARG cc_start: 0.3525 (mtt90) cc_final: 0.3215 (tpp-160) REVERT: B 134 ASP cc_start: 0.5199 (p0) cc_final: 0.3807 (t0) REVERT: C 89 ARG cc_start: 0.6271 (ptp90) cc_final: 0.5797 (ptm-80) REVERT: C 322 GLU cc_start: 0.7623 (tp30) cc_final: 0.7185 (mt-10) REVERT: C 334 ASN cc_start: 0.7870 (m-40) cc_final: 0.7602 (m110) REVERT: C 342 SER cc_start: 0.6314 (OUTLIER) cc_final: 0.5804 (m) REVERT: C 544 CYS cc_start: 0.4631 (OUTLIER) cc_final: 0.3420 (m) REVERT: C 553 ARG cc_start: 0.7693 (mpt180) cc_final: 0.7120 (tpt-90) REVERT: D 72 MET cc_start: 0.1484 (tmm) cc_final: 0.1118 (tmm) REVERT: D 73 MET cc_start: -0.2785 (mmt) cc_final: -0.3050 (ttt) REVERT: D 134 ASP cc_start: 0.5293 (p0) cc_final: 0.3893 (t0) REVERT: D 142 PHE cc_start: 0.6877 (t80) cc_final: 0.6511 (t80) REVERT: D 146 MET cc_start: 0.6392 (mmm) cc_final: 0.6101 (mmm) REVERT: E 89 ARG cc_start: 0.6259 (ptp90) cc_final: 0.5777 (ptm-80) REVERT: E 123 GLU cc_start: 0.6775 (tp30) cc_final: 0.5761 (tm-30) REVERT: E 176 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7229 (mp) REVERT: E 322 GLU cc_start: 0.7570 (tp30) cc_final: 0.7139 (mt-10) REVERT: E 334 ASN cc_start: 0.7924 (m-40) cc_final: 0.7635 (m110) REVERT: E 342 SER cc_start: 0.6129 (OUTLIER) cc_final: 0.5654 (m) REVERT: E 544 CYS cc_start: 0.5076 (OUTLIER) cc_final: 0.3891 (m) REVERT: E 553 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7372 (tmt170) REVERT: E 570 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7646 (tm-30) REVERT: F 72 MET cc_start: -0.0248 (ptt) cc_final: -0.0611 (tmm) REVERT: F 73 MET cc_start: -0.2260 (mmm) cc_final: -0.2589 (ttm) REVERT: F 134 ASP cc_start: 0.5205 (p0) cc_final: 0.3799 (t0) REVERT: F 142 PHE cc_start: 0.6802 (t80) cc_final: 0.6443 (t80) REVERT: F 146 MET cc_start: 0.6349 (mmm) cc_final: 0.5971 (mmm) REVERT: G 89 ARG cc_start: 0.6437 (ptp90) cc_final: 0.5927 (ptm-80) REVERT: G 322 GLU cc_start: 0.7722 (tp30) cc_final: 0.7291 (mt-10) REVERT: G 334 ASN cc_start: 0.7935 (m-40) cc_final: 0.7651 (m110) REVERT: G 342 SER cc_start: 0.6263 (OUTLIER) cc_final: 0.5758 (m) REVERT: G 544 CYS cc_start: 0.4950 (OUTLIER) cc_final: 0.3953 (m) REVERT: G 553 ARG cc_start: 0.7663 (mpt180) cc_final: 0.7110 (tpt-90) REVERT: H 72 MET cc_start: -0.0440 (ptt) cc_final: -0.0788 (tmm) REVERT: H 73 MET cc_start: -0.1837 (tpt) cc_final: -0.2816 (ttm) REVERT: H 134 ASP cc_start: 0.5241 (p0) cc_final: 0.3820 (t0) outliers start: 35 outliers final: 15 residues processed: 248 average time/residue: 2.3519 time to fit residues: 653.0324 Evaluate side-chains 235 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 50.0000 chunk 112 optimal weight: 0.0870 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15504 Z= 0.189 Angle : 0.492 5.937 20912 Z= 0.261 Chirality : 0.033 0.117 2288 Planarity : 0.003 0.032 2636 Dihedral : 4.324 50.583 2078 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.40 % Allowed : 23.48 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 1848 helix: 2.23 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.96 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 91 HIS 0.003 0.001 HIS C 575 PHE 0.012 0.001 PHE C 329 TYR 0.009 0.001 TYR A 74 ARG 0.006 0.000 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 262 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 224 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6286 (ptp90) cc_final: 0.5870 (ptm-80) REVERT: A 322 GLU cc_start: 0.7533 (tp30) cc_final: 0.7100 (mt-10) REVERT: A 334 ASN cc_start: 0.7879 (m-40) cc_final: 0.7635 (m110) REVERT: A 342 SER cc_start: 0.6189 (OUTLIER) cc_final: 0.5640 (m) REVERT: A 544 CYS cc_start: 0.5173 (OUTLIER) cc_final: 0.3814 (m) REVERT: A 553 ARG cc_start: 0.7612 (mpt180) cc_final: 0.7027 (tpt-90) REVERT: B 91 ARG cc_start: 0.8300 (ptm160) cc_final: 0.8092 (ptm-80) REVERT: B 107 ARG cc_start: 0.3529 (mtt90) cc_final: 0.3281 (tpp-160) REVERT: B 134 ASP cc_start: 0.4935 (p0) cc_final: 0.3600 (t0) REVERT: C 89 ARG cc_start: 0.6349 (ptp90) cc_final: 0.5893 (ptm-80) REVERT: C 322 GLU cc_start: 0.7615 (tp30) cc_final: 0.7184 (mt-10) REVERT: C 334 ASN cc_start: 0.7865 (m-40) cc_final: 0.7606 (m110) REVERT: C 342 SER cc_start: 0.6309 (OUTLIER) cc_final: 0.5819 (m) REVERT: C 544 CYS cc_start: 0.4647 (OUTLIER) cc_final: 0.3424 (m) REVERT: C 553 ARG cc_start: 0.7679 (mpt180) cc_final: 0.7123 (tpt-90) REVERT: D 72 MET cc_start: 0.1487 (tmm) cc_final: 0.1260 (tmm) REVERT: D 73 MET cc_start: -0.2764 (mmt) cc_final: -0.3012 (ttt) REVERT: D 134 ASP cc_start: 0.5187 (p0) cc_final: 0.3733 (t0) REVERT: D 142 PHE cc_start: 0.7004 (t80) cc_final: 0.6746 (t80) REVERT: D 143 VAL cc_start: 0.5816 (m) cc_final: 0.5567 (p) REVERT: E 89 ARG cc_start: 0.6345 (ptp90) cc_final: 0.5876 (ptm-80) REVERT: E 123 GLU cc_start: 0.6703 (tp30) cc_final: 0.5682 (tm-30) REVERT: E 176 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7181 (mp) REVERT: E 322 GLU cc_start: 0.7543 (tp30) cc_final: 0.7203 (mt-10) REVERT: E 334 ASN cc_start: 0.7920 (m-40) cc_final: 0.7637 (m110) REVERT: E 342 SER cc_start: 0.6284 (OUTLIER) cc_final: 0.5754 (m) REVERT: E 544 CYS cc_start: 0.4996 (OUTLIER) cc_final: 0.3811 (m) REVERT: E 553 ARG cc_start: 0.7659 (mpt180) cc_final: 0.7081 (tpt-90) REVERT: F 72 MET cc_start: 0.0217 (ptt) cc_final: -0.0161 (tmm) REVERT: F 73 MET cc_start: -0.2119 (mmm) cc_final: -0.2467 (ttm) REVERT: F 90 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7343 (t80) REVERT: F 91 ARG cc_start: 0.8523 (ptm160) cc_final: 0.8050 (ptm160) REVERT: F 134 ASP cc_start: 0.4995 (p0) cc_final: 0.3607 (t0) REVERT: F 142 PHE cc_start: 0.6968 (t80) cc_final: 0.6624 (t80) REVERT: F 146 MET cc_start: 0.6531 (mmm) cc_final: 0.6128 (mmm) REVERT: G 89 ARG cc_start: 0.6373 (ptp90) cc_final: 0.5929 (ptm-80) REVERT: G 123 GLU cc_start: 0.6374 (tp30) cc_final: 0.5652 (tt0) REVERT: G 322 GLU cc_start: 0.7681 (tp30) cc_final: 0.7238 (mt-10) REVERT: G 334 ASN cc_start: 0.7920 (m-40) cc_final: 0.7623 (m110) REVERT: G 342 SER cc_start: 0.6269 (OUTLIER) cc_final: 0.5747 (m) REVERT: G 544 CYS cc_start: 0.5053 (OUTLIER) cc_final: 0.3967 (m) REVERT: G 553 ARG cc_start: 0.7634 (mpt180) cc_final: 0.7138 (tpt-90) REVERT: H 72 MET cc_start: -0.0492 (OUTLIER) cc_final: -0.0871 (tmm) REVERT: H 73 MET cc_start: -0.1855 (tpt) cc_final: -0.2843 (ttm) REVERT: H 91 ARG cc_start: 0.8472 (ptm160) cc_final: 0.8098 (ptm160) REVERT: H 134 ASP cc_start: 0.5022 (p0) cc_final: 0.3624 (t0) outliers start: 38 outliers final: 11 residues processed: 254 average time/residue: 2.2712 time to fit residues: 647.8780 Evaluate side-chains 238 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 216 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15504 Z= 0.424 Angle : 0.571 6.622 20912 Z= 0.310 Chirality : 0.037 0.149 2288 Planarity : 0.004 0.037 2636 Dihedral : 4.510 51.728 2078 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.90 % Allowed : 23.99 % Favored : 73.11 % 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: 2.20 (0.19), residues: 1848 helix: 2.04 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 344 HIS 0.005 0.001 HIS G 96 PHE 0.022 0.002 PHE C 329 TYR 0.017 0.001 TYR A 74 ARG 0.007 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 272 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6545 (ptp90) cc_final: 0.5977 (ptm-80) REVERT: A 123 GLU cc_start: 0.6525 (tp30) cc_final: 0.5872 (tt0) REVERT: A 322 GLU cc_start: 0.7572 (tp30) cc_final: 0.7170 (mt-10) REVERT: A 342 SER cc_start: 0.6111 (OUTLIER) cc_final: 0.5579 (m) REVERT: A 544 CYS cc_start: 0.5212 (OUTLIER) cc_final: 0.3847 (m) REVERT: A 553 ARG cc_start: 0.7631 (mpt180) cc_final: 0.6987 (tpt-90) REVERT: B 77 MET cc_start: 0.2050 (OUTLIER) cc_final: 0.1752 (mmt) REVERT: B 91 ARG cc_start: 0.8353 (ptm160) cc_final: 0.8150 (ptm-80) REVERT: B 107 ARG cc_start: 0.3454 (mtt90) cc_final: 0.3135 (tpp-160) REVERT: B 134 ASP cc_start: 0.5269 (p0) cc_final: 0.3619 (t0) REVERT: C 89 ARG cc_start: 0.6394 (ptp90) cc_final: 0.5876 (ptm-80) REVERT: C 123 GLU cc_start: 0.6619 (tp30) cc_final: 0.5975 (tt0) REVERT: C 322 GLU cc_start: 0.7598 (tp30) cc_final: 0.7176 (mt-10) REVERT: C 342 SER cc_start: 0.6268 (OUTLIER) cc_final: 0.5803 (m) REVERT: C 544 CYS cc_start: 0.5044 (OUTLIER) cc_final: 0.3617 (m) REVERT: C 553 ARG cc_start: 0.7606 (mpt180) cc_final: 0.7040 (tpt-90) REVERT: D 73 MET cc_start: -0.2842 (mmt) cc_final: -0.3054 (ttt) REVERT: E 89 ARG cc_start: 0.6475 (ptp90) cc_final: 0.5909 (ptm-80) REVERT: E 123 GLU cc_start: 0.6631 (tp30) cc_final: 0.5733 (tm-30) REVERT: E 176 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7260 (mp) REVERT: E 322 GLU cc_start: 0.7646 (tp30) cc_final: 0.7099 (mt-10) REVERT: E 334 ASN cc_start: 0.7915 (m-40) cc_final: 0.7633 (m110) REVERT: E 342 SER cc_start: 0.6377 (OUTLIER) cc_final: 0.5918 (m) REVERT: E 544 CYS cc_start: 0.5019 (OUTLIER) cc_final: 0.3963 (m) REVERT: E 546 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5500 (mmp) REVERT: E 553 ARG cc_start: 0.7577 (mpt180) cc_final: 0.6994 (tpt-90) REVERT: F 72 MET cc_start: -0.0162 (ptt) cc_final: -0.0473 (tmm) REVERT: F 73 MET cc_start: -0.2145 (mmm) cc_final: -0.2536 (ttm) REVERT: F 90 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7264 (t80) REVERT: F 91 ARG cc_start: 0.8524 (ptm160) cc_final: 0.8077 (ptm160) REVERT: F 134 ASP cc_start: 0.5234 (p0) cc_final: 0.3684 (t0) REVERT: F 142 PHE cc_start: 0.6916 (t80) cc_final: 0.6551 (t80) REVERT: F 146 MET cc_start: 0.6453 (mmm) cc_final: 0.6222 (mmm) REVERT: G 89 ARG cc_start: 0.6583 (ptp90) cc_final: 0.6088 (ptm-80) REVERT: G 123 GLU cc_start: 0.6559 (tp30) cc_final: 0.5901 (tt0) REVERT: G 322 GLU cc_start: 0.7734 (tp30) cc_final: 0.7317 (mt-10) REVERT: G 334 ASN cc_start: 0.7892 (m-40) cc_final: 0.7623 (m110) REVERT: G 342 SER cc_start: 0.6287 (OUTLIER) cc_final: 0.5791 (m) REVERT: G 544 CYS cc_start: 0.4999 (OUTLIER) cc_final: 0.3926 (m) REVERT: G 553 ARG cc_start: 0.7563 (mpt180) cc_final: 0.7088 (tpt-90) REVERT: H 72 MET cc_start: -0.0753 (OUTLIER) cc_final: -0.1108 (tmm) REVERT: H 73 MET cc_start: -0.1887 (tpt) cc_final: -0.2872 (ttm) REVERT: H 91 ARG cc_start: 0.8539 (ptm160) cc_final: 0.8166 (ptm160) REVERT: H 134 ASP cc_start: 0.5258 (p0) cc_final: 0.3572 (t0) outliers start: 46 outliers final: 15 residues processed: 262 average time/residue: 2.2380 time to fit residues: 659.2544 Evaluate side-chains 237 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15504 Z= 0.198 Angle : 0.515 7.134 20912 Z= 0.271 Chirality : 0.034 0.120 2288 Planarity : 0.003 0.033 2636 Dihedral : 4.454 51.053 2078 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.27 % Allowed : 24.94 % Favored : 72.79 % 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: 2.51 (0.19), residues: 1848 helix: 2.29 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 270 HIS 0.004 0.001 HIS H 108 PHE 0.012 0.001 PHE C 329 TYR 0.009 0.001 TYR A 74 ARG 0.004 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 256 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6280 (ptp90) cc_final: 0.5901 (ptm-80) REVERT: A 123 GLU cc_start: 0.6438 (tp30) cc_final: 0.5796 (tt0) REVERT: A 322 GLU cc_start: 0.7549 (tp30) cc_final: 0.7141 (mt-10) REVERT: A 334 ASN cc_start: 0.7901 (m-40) cc_final: 0.7660 (m110) REVERT: A 544 CYS cc_start: 0.5251 (OUTLIER) cc_final: 0.3835 (m) REVERT: A 553 ARG cc_start: 0.7582 (mpt180) cc_final: 0.6803 (tpp80) REVERT: B 32 GLU cc_start: 0.5729 (mt-10) cc_final: 0.5295 (mm-30) REVERT: B 91 ARG cc_start: 0.8320 (ptm160) cc_final: 0.8090 (ptm-80) REVERT: B 107 ARG cc_start: 0.3398 (mtt90) cc_final: 0.3196 (tpt-90) REVERT: B 134 ASP cc_start: 0.5144 (p0) cc_final: 0.3539 (m-30) REVERT: C 89 ARG cc_start: 0.6236 (ptp90) cc_final: 0.5874 (ptm-80) REVERT: C 123 GLU cc_start: 0.6556 (tp30) cc_final: 0.5926 (tt0) REVERT: C 322 GLU cc_start: 0.7606 (tp30) cc_final: 0.7177 (mt-10) REVERT: C 334 ASN cc_start: 0.7885 (m-40) cc_final: 0.7606 (m110) REVERT: C 342 SER cc_start: 0.6290 (OUTLIER) cc_final: 0.5791 (m) REVERT: C 544 CYS cc_start: 0.4804 (OUTLIER) cc_final: 0.3509 (m) REVERT: C 553 ARG cc_start: 0.7626 (mpt180) cc_final: 0.7057 (tpt-90) REVERT: D 72 MET cc_start: 0.1539 (tmm) cc_final: 0.1229 (tmm) REVERT: D 73 MET cc_start: -0.2769 (mmt) cc_final: -0.3014 (ttt) REVERT: D 90 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7179 (t80) REVERT: E 89 ARG cc_start: 0.6343 (ptp90) cc_final: 0.5931 (ptm-80) REVERT: E 123 GLU cc_start: 0.6685 (tp30) cc_final: 0.5731 (tm-30) REVERT: E 176 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7193 (mp) REVERT: E 322 GLU cc_start: 0.7538 (tp30) cc_final: 0.7215 (mt-10) REVERT: E 334 ASN cc_start: 0.7935 (m-40) cc_final: 0.7641 (m110) REVERT: E 544 CYS cc_start: 0.4993 (OUTLIER) cc_final: 0.3985 (m) REVERT: E 553 ARG cc_start: 0.7597 (mpt180) cc_final: 0.6935 (tmm-80) REVERT: F 72 MET cc_start: -0.0131 (ptt) cc_final: -0.0480 (tmm) REVERT: F 73 MET cc_start: -0.2209 (mmm) cc_final: -0.2602 (ttm) REVERT: F 90 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7291 (t80) REVERT: F 91 ARG cc_start: 0.8468 (ptm160) cc_final: 0.8044 (ptm160) REVERT: F 134 ASP cc_start: 0.5119 (p0) cc_final: 0.3552 (t0) REVERT: F 142 PHE cc_start: 0.6922 (t80) cc_final: 0.6541 (t80) REVERT: F 146 MET cc_start: 0.6477 (mmm) cc_final: 0.6234 (mmm) REVERT: G 89 ARG cc_start: 0.6458 (ptp90) cc_final: 0.5988 (ptm-80) REVERT: G 123 GLU cc_start: 0.6433 (tp30) cc_final: 0.5779 (tt0) REVERT: G 322 GLU cc_start: 0.7671 (tp30) cc_final: 0.7248 (mt-10) REVERT: G 334 ASN cc_start: 0.7930 (m-40) cc_final: 0.7661 (m110) REVERT: G 544 CYS cc_start: 0.5075 (OUTLIER) cc_final: 0.4003 (m) REVERT: G 553 ARG cc_start: 0.7575 (mpt180) cc_final: 0.7088 (tpt-90) REVERT: H 72 MET cc_start: -0.0535 (OUTLIER) cc_final: -0.0934 (tmm) REVERT: H 73 MET cc_start: -0.1856 (tpt) cc_final: -0.2850 (ttm) REVERT: H 91 ARG cc_start: 0.8451 (ptm160) cc_final: 0.8079 (ptm160) REVERT: H 134 ASP cc_start: 0.5181 (p0) cc_final: 0.3566 (t0) outliers start: 36 outliers final: 14 residues processed: 246 average time/residue: 2.4618 time to fit residues: 675.9133 Evaluate side-chains 232 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 40.0000 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15504 Z= 0.338 Angle : 0.554 7.572 20912 Z= 0.295 Chirality : 0.035 0.136 2288 Planarity : 0.004 0.035 2636 Dihedral : 4.315 51.812 2075 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.65 % Allowed : 25.06 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.19), residues: 1848 helix: 2.23 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.10 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 91 HIS 0.004 0.001 HIS G 96 PHE 0.018 0.001 PHE C 329 TYR 0.014 0.001 TYR A 74 ARG 0.004 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 250 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6370 (ptp90) cc_final: 0.5858 (ptm-80) REVERT: A 123 GLU cc_start: 0.6514 (tp30) cc_final: 0.5877 (tt0) REVERT: A 322 GLU cc_start: 0.7574 (tp30) cc_final: 0.7172 (mt-10) REVERT: A 544 CYS cc_start: 0.5187 (OUTLIER) cc_final: 0.3813 (m) REVERT: A 553 ARG cc_start: 0.7603 (mpt180) cc_final: 0.6805 (tpp80) REVERT: A 570 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 90 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7387 (t80) REVERT: B 107 ARG cc_start: 0.3597 (mtt90) cc_final: 0.3384 (tpp-160) REVERT: B 134 ASP cc_start: 0.5195 (p0) cc_final: 0.3480 (m-30) REVERT: C 89 ARG cc_start: 0.6394 (ptp90) cc_final: 0.5938 (ptm-80) REVERT: C 123 GLU cc_start: 0.6527 (tp30) cc_final: 0.5925 (tt0) REVERT: C 322 GLU cc_start: 0.7617 (tp30) cc_final: 0.7208 (mt-10) REVERT: C 544 CYS cc_start: 0.4889 (OUTLIER) cc_final: 0.3534 (m) REVERT: C 553 ARG cc_start: 0.7620 (mpt180) cc_final: 0.7044 (tpt-90) REVERT: C 565 MET cc_start: 0.7469 (tpt) cc_final: 0.7015 (ptm) REVERT: D 72 MET cc_start: 0.1343 (tmm) cc_final: 0.1050 (tmm) REVERT: D 73 MET cc_start: -0.2797 (mmt) cc_final: -0.3003 (ttt) REVERT: D 90 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7182 (t80) REVERT: E 89 ARG cc_start: 0.6331 (ptp90) cc_final: 0.5832 (ptm-80) REVERT: E 123 GLU cc_start: 0.6644 (tp30) cc_final: 0.5731 (tm-30) REVERT: E 176 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7231 (mp) REVERT: E 322 GLU cc_start: 0.7636 (tp30) cc_final: 0.7221 (mt-10) REVERT: E 334 ASN cc_start: 0.7859 (m-40) cc_final: 0.7574 (m110) REVERT: E 342 SER cc_start: 0.6339 (OUTLIER) cc_final: 0.5845 (m) REVERT: E 544 CYS cc_start: 0.4891 (OUTLIER) cc_final: 0.3892 (m) REVERT: E 553 ARG cc_start: 0.7569 (mpt180) cc_final: 0.7292 (tmt170) REVERT: F 72 MET cc_start: -0.0208 (ptt) cc_final: -0.0499 (tmm) REVERT: F 73 MET cc_start: -0.2186 (mmm) cc_final: -0.2612 (ttm) REVERT: F 90 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7270 (t80) REVERT: F 91 ARG cc_start: 0.8453 (ptm160) cc_final: 0.8035 (ptm160) REVERT: F 134 ASP cc_start: 0.5191 (p0) cc_final: 0.3578 (m-30) REVERT: F 142 PHE cc_start: 0.6903 (t80) cc_final: 0.6498 (t80) REVERT: G 89 ARG cc_start: 0.6568 (ptp90) cc_final: 0.6081 (ptm-80) REVERT: G 123 GLU cc_start: 0.6548 (tp30) cc_final: 0.5905 (tt0) REVERT: G 176 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7081 (mp) REVERT: G 322 GLU cc_start: 0.7725 (tp30) cc_final: 0.7309 (mt-10) REVERT: G 334 ASN cc_start: 0.7836 (m-40) cc_final: 0.7605 (m110) REVERT: G 342 SER cc_start: 0.6304 (OUTLIER) cc_final: 0.5800 (m) REVERT: G 544 CYS cc_start: 0.5006 (OUTLIER) cc_final: 0.3933 (m) REVERT: G 553 ARG cc_start: 0.7569 (mpt180) cc_final: 0.7075 (tpt-90) REVERT: H 72 MET cc_start: -0.0754 (OUTLIER) cc_final: -0.1112 (tmm) REVERT: H 73 MET cc_start: -0.1907 (tpt) cc_final: -0.2869 (ttm) REVERT: H 90 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7335 (t80) REVERT: H 91 ARG cc_start: 0.8465 (ptm160) cc_final: 0.8075 (ptm160) outliers start: 42 outliers final: 17 residues processed: 234 average time/residue: 2.5622 time to fit residues: 666.2738 Evaluate side-chains 233 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 570 GLN Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 40.0000 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15504 Z= 0.175 Angle : 0.517 8.561 20912 Z= 0.268 Chirality : 0.033 0.120 2288 Planarity : 0.003 0.033 2636 Dihedral : 4.154 51.231 2074 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.96 % Allowed : 25.51 % Favored : 72.54 % 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: 2.69 (0.19), residues: 1848 helix: 2.43 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.003 0.001 HIS C 575 PHE 0.012 0.001 PHE C 100 TYR 0.008 0.001 TYR A 74 ARG 0.005 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6255 (ptp90) cc_final: 0.5867 (ptm-80) REVERT: A 123 GLU cc_start: 0.6518 (tp30) cc_final: 0.5853 (tt0) REVERT: A 322 GLU cc_start: 0.7565 (tp30) cc_final: 0.7164 (mt-10) REVERT: A 342 SER cc_start: 0.6092 (OUTLIER) cc_final: 0.5518 (m) REVERT: A 544 CYS cc_start: 0.5126 (OUTLIER) cc_final: 0.3808 (m) REVERT: A 553 ARG cc_start: 0.7585 (mpt180) cc_final: 0.6826 (tpp80) REVERT: A 570 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 107 ARG cc_start: 0.3545 (mtt90) cc_final: 0.3338 (tpp-160) REVERT: B 134 ASP cc_start: 0.4937 (p0) cc_final: 0.3307 (m-30) REVERT: C 89 ARG cc_start: 0.6240 (ptp90) cc_final: 0.5783 (ptm-80) REVERT: C 123 GLU cc_start: 0.6552 (tp30) cc_final: 0.5950 (tt0) REVERT: C 322 GLU cc_start: 0.7600 (tp30) cc_final: 0.7188 (mt-10) REVERT: C 544 CYS cc_start: 0.4820 (OUTLIER) cc_final: 0.3411 (m) REVERT: C 553 ARG cc_start: 0.7625 (mpt180) cc_final: 0.7031 (tpt-90) REVERT: D 72 MET cc_start: 0.1418 (tmm) cc_final: 0.1202 (tmm) REVERT: D 90 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7227 (t80) REVERT: E 89 ARG cc_start: 0.6213 (ptp90) cc_final: 0.5842 (ptm-80) REVERT: E 123 GLU cc_start: 0.6678 (tp30) cc_final: 0.5735 (tm-30) REVERT: E 176 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7177 (mp) REVERT: E 322 GLU cc_start: 0.7622 (tp30) cc_final: 0.7207 (mt-10) REVERT: E 334 ASN cc_start: 0.7870 (m-40) cc_final: 0.7590 (m110) REVERT: E 342 SER cc_start: 0.6302 (OUTLIER) cc_final: 0.5767 (m) REVERT: E 544 CYS cc_start: 0.4997 (OUTLIER) cc_final: 0.3959 (m) REVERT: E 553 ARG cc_start: 0.7563 (mpt180) cc_final: 0.6999 (tpt-90) REVERT: F 72 MET cc_start: -0.0120 (ptt) cc_final: -0.0356 (tmm) REVERT: F 73 MET cc_start: -0.2264 (mmm) cc_final: -0.2751 (ttm) REVERT: F 90 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7296 (t80) REVERT: F 91 ARG cc_start: 0.8422 (ptm160) cc_final: 0.7997 (ptm160) REVERT: F 134 ASP cc_start: 0.4883 (p0) cc_final: 0.3366 (t0) REVERT: G 89 ARG cc_start: 0.6427 (ptp90) cc_final: 0.5964 (ptm-80) REVERT: G 123 GLU cc_start: 0.6554 (tp30) cc_final: 0.5881 (tt0) REVERT: G 176 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7019 (mp) REVERT: G 334 ASN cc_start: 0.7870 (m-40) cc_final: 0.7614 (m110) REVERT: G 342 SER cc_start: 0.6331 (OUTLIER) cc_final: 0.5806 (m) REVERT: G 544 CYS cc_start: 0.4965 (OUTLIER) cc_final: 0.3801 (m) REVERT: G 553 ARG cc_start: 0.7561 (mpt180) cc_final: 0.6855 (tpp80) REVERT: H 72 MET cc_start: -0.0741 (OUTLIER) cc_final: -0.1096 (tmm) REVERT: H 73 MET cc_start: -0.2077 (tpt) cc_final: -0.3033 (ttm) REVERT: H 90 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7318 (t80) REVERT: H 91 ARG cc_start: 0.8430 (ptm160) cc_final: 0.8015 (ptm160) REVERT: H 134 ASP cc_start: 0.4999 (p0) cc_final: 0.3359 (t0) outliers start: 31 outliers final: 11 residues processed: 236 average time/residue: 2.4779 time to fit residues: 652.9510 Evaluate side-chains 234 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15504 Z= 0.353 Angle : 0.569 8.898 20912 Z= 0.302 Chirality : 0.036 0.140 2288 Planarity : 0.004 0.034 2636 Dihedral : 4.229 52.015 2074 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.15 % Allowed : 25.25 % Favored : 72.60 % 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: 2.52 (0.19), residues: 1848 helix: 2.30 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.09 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 344 HIS 0.004 0.001 HIS G 96 PHE 0.019 0.002 PHE C 329 TYR 0.014 0.001 TYR A 74 ARG 0.006 0.000 ARG G 581 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 240 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 206 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6399 (ptp90) cc_final: 0.5951 (ptm-80) REVERT: A 123 GLU cc_start: 0.6513 (tp30) cc_final: 0.5887 (tt0) REVERT: A 322 GLU cc_start: 0.7574 (tp30) cc_final: 0.7178 (mt-10) REVERT: A 544 CYS cc_start: 0.5088 (OUTLIER) cc_final: 0.3802 (m) REVERT: A 553 ARG cc_start: 0.7623 (mpt180) cc_final: 0.6836 (tpp80) REVERT: B 90 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7229 (t80) REVERT: B 107 ARG cc_start: 0.3666 (mtt90) cc_final: 0.3455 (tpp-160) REVERT: C 89 ARG cc_start: 0.6387 (ptp90) cc_final: 0.5959 (ptm-80) REVERT: C 322 GLU cc_start: 0.7621 (tp30) cc_final: 0.7208 (mt-10) REVERT: C 544 CYS cc_start: 0.4874 (OUTLIER) cc_final: 0.3488 (m) REVERT: D 90 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7214 (t80) REVERT: E 89 ARG cc_start: 0.6355 (ptp90) cc_final: 0.5930 (ptm-80) REVERT: E 123 GLU cc_start: 0.6685 (tp30) cc_final: 0.5768 (tm-30) REVERT: E 176 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7204 (mp) REVERT: E 322 GLU cc_start: 0.7642 (tp30) cc_final: 0.7216 (mt-10) REVERT: E 342 SER cc_start: 0.6265 (OUTLIER) cc_final: 0.5751 (m) REVERT: E 544 CYS cc_start: 0.4909 (OUTLIER) cc_final: 0.3920 (m) REVERT: E 553 ARG cc_start: 0.7600 (mpt180) cc_final: 0.7270 (tmt170) REVERT: F 72 MET cc_start: -0.0152 (ptt) cc_final: -0.0379 (tmm) REVERT: F 73 MET cc_start: -0.2238 (mmm) cc_final: -0.2714 (ttm) REVERT: F 90 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7258 (t80) REVERT: F 91 ARG cc_start: 0.8445 (ptm160) cc_final: 0.8018 (ptm160) REVERT: F 134 ASP cc_start: 0.5057 (p0) cc_final: 0.3442 (m-30) REVERT: G 89 ARG cc_start: 0.6560 (ptp90) cc_final: 0.6092 (ptm-80) REVERT: G 123 GLU cc_start: 0.6550 (tp30) cc_final: 0.5918 (tt0) REVERT: G 176 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7062 (mp) REVERT: G 322 GLU cc_start: 0.7720 (tp30) cc_final: 0.7306 (mt-10) REVERT: G 334 ASN cc_start: 0.7838 (m-40) cc_final: 0.7597 (m110) REVERT: G 342 SER cc_start: 0.6307 (OUTLIER) cc_final: 0.5783 (m) REVERT: G 544 CYS cc_start: 0.5097 (OUTLIER) cc_final: 0.3953 (m) REVERT: G 553 ARG cc_start: 0.7581 (mpt180) cc_final: 0.6860 (tpp80) REVERT: H 72 MET cc_start: -0.0826 (OUTLIER) cc_final: -0.1164 (tmm) REVERT: H 73 MET cc_start: -0.2033 (tpt) cc_final: -0.3036 (ttt) REVERT: H 90 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7369 (t80) REVERT: H 91 ARG cc_start: 0.8431 (ptm160) cc_final: 0.8019 (ptm160) outliers start: 34 outliers final: 15 residues processed: 226 average time/residue: 2.4047 time to fit residues: 607.3027 Evaluate side-chains 226 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15504 Z= 0.260 Angle : 0.548 9.501 20912 Z= 0.287 Chirality : 0.034 0.121 2288 Planarity : 0.004 0.033 2636 Dihedral : 4.260 51.877 2074 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.96 % Allowed : 25.51 % Favored : 72.54 % 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: 2.60 (0.19), residues: 1848 helix: 2.36 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.06 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 344 HIS 0.003 0.001 HIS G 96 PHE 0.015 0.001 PHE C 329 TYR 0.011 0.001 TYR A 74 ARG 0.004 0.000 ARG G 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 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 347 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 347 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 347 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 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6345 (ptp90) cc_final: 0.5907 (ptm-80) REVERT: A 123 GLU cc_start: 0.6495 (tp30) cc_final: 0.5868 (tt0) REVERT: A 322 GLU cc_start: 0.7581 (tp30) cc_final: 0.7187 (mt-10) REVERT: A 342 SER cc_start: 0.6111 (OUTLIER) cc_final: 0.5592 (m) REVERT: A 544 CYS cc_start: 0.5065 (OUTLIER) cc_final: 0.3730 (m) REVERT: A 553 ARG cc_start: 0.7620 (mpt180) cc_final: 0.6836 (tpp80) REVERT: A 570 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 90 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7266 (t80) REVERT: B 107 ARG cc_start: 0.3620 (mtt90) cc_final: 0.3415 (tpp-160) REVERT: C 89 ARG cc_start: 0.6394 (ptp90) cc_final: 0.5981 (ptm-80) REVERT: C 123 GLU cc_start: 0.6540 (tp30) cc_final: 0.5915 (tt0) REVERT: C 322 GLU cc_start: 0.7607 (tp30) cc_final: 0.7195 (mt-10) REVERT: C 342 SER cc_start: 0.6140 (OUTLIER) cc_final: 0.5665 (m) REVERT: C 544 CYS cc_start: 0.4974 (OUTLIER) cc_final: 0.3555 (m) REVERT: D 90 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7237 (t80) REVERT: E 89 ARG cc_start: 0.6294 (ptp90) cc_final: 0.5879 (ptm-80) REVERT: E 123 GLU cc_start: 0.6669 (tp30) cc_final: 0.5755 (tm-30) REVERT: E 176 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7197 (mp) REVERT: E 322 GLU cc_start: 0.7620 (tp30) cc_final: 0.7202 (mt-10) REVERT: E 342 SER cc_start: 0.6268 (OUTLIER) cc_final: 0.5745 (m) REVERT: E 544 CYS cc_start: 0.5003 (OUTLIER) cc_final: 0.3980 (m) REVERT: E 553 ARG cc_start: 0.7604 (mpt180) cc_final: 0.7263 (tmt170) REVERT: F 72 MET cc_start: -0.0153 (ptt) cc_final: -0.0390 (tmm) REVERT: F 73 MET cc_start: -0.2227 (mmm) cc_final: -0.2746 (ttm) REVERT: F 90 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7286 (t80) REVERT: F 91 ARG cc_start: 0.8433 (ptm160) cc_final: 0.8011 (ptm160) REVERT: F 134 ASP cc_start: 0.5020 (p0) cc_final: 0.3353 (m-30) REVERT: G 89 ARG cc_start: 0.6449 (ptp90) cc_final: 0.5983 (ptm-80) REVERT: G 123 GLU cc_start: 0.6524 (tp30) cc_final: 0.5906 (tt0) REVERT: G 176 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7031 (mp) REVERT: G 322 GLU cc_start: 0.7691 (tp30) cc_final: 0.7275 (mt-10) REVERT: G 334 ASN cc_start: 0.7785 (m-40) cc_final: 0.7534 (m110) REVERT: G 342 SER cc_start: 0.6266 (OUTLIER) cc_final: 0.5732 (m) REVERT: G 544 CYS cc_start: 0.5099 (OUTLIER) cc_final: 0.3910 (m) REVERT: G 553 ARG cc_start: 0.7595 (mpt180) cc_final: 0.6867 (tpp80) REVERT: H 72 MET cc_start: -0.0789 (OUTLIER) cc_final: -0.1096 (tmm) REVERT: H 73 MET cc_start: -0.2147 (tpt) cc_final: -0.3138 (ttt) REVERT: H 90 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7400 (t80) outliers start: 31 outliers final: 13 residues processed: 226 average time/residue: 2.4468 time to fit residues: 615.3637 Evaluate side-chains 230 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 570 GLN Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.225971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126581 restraints weight = 56111.830| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.25 r_work: 0.3383 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 15504 Z= 0.270 Angle : 0.757 59.171 20912 Z= 0.427 Chirality : 0.034 0.121 2288 Planarity : 0.004 0.034 2636 Dihedral : 4.253 51.877 2074 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.96 % Allowed : 25.69 % Favored : 72.35 % 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: 2.62 (0.19), residues: 1848 helix: 2.37 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.06 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 344 HIS 0.003 0.001 HIS G 96 PHE 0.014 0.001 PHE C 329 TYR 0.011 0.001 TYR A 74 ARG 0.002 0.000 ARG H 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11779.50 seconds wall clock time: 204 minutes 29.15 seconds (12269.15 seconds total)