Starting phenix.real_space_refine on Fri Sep 27 06:34:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vm3_21237/09_2024/6vm3_21237.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vm3_21237/09_2024/6vm3_21237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vm3_21237/09_2024/6vm3_21237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vm3_21237/09_2024/6vm3_21237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vm3_21237/09_2024/6vm3_21237.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vm3_21237/09_2024/6vm3_21237.cif" } resolution = 3.07 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9900 2.51 5 N 2435 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15180 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "E" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "C" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "D" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2942 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 1 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IVM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.21, per 1000 atoms: 0.61 Number of scatterers: 15180 At special positions: 0 Unit cell: (95.76, 96.6, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2745 8.00 N 2435 7.00 C 9900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 20 sheets defined 39.5% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.561A pdb=" N SER A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 340 Processing helix chain 'A' and resid 395 through 444 removed outlier: 3.814A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'E' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.562A pdb=" N SER E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 340 Processing helix chain 'E' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL E 416 " --> pdb=" O THR E 412 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'C' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.561A pdb=" N SER C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 340 Processing helix chain 'C' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.572A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.562A pdb=" N SER B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 340 Processing helix chain 'B' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'D' and resid 33 through 42 removed outlier: 3.573A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.543A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 265 removed outlier: 3.561A pdb=" N SER D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.757A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 340 Processing helix chain 'D' and resid 395 through 444 removed outlier: 3.813A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 removed outlier: 8.069A pdb=" N CYS A 233 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG A 220 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 235 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP A 218 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG A 237 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU A 216 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS A 239 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 123 through 124 removed outlier: 8.070A pdb=" N CYS E 233 " --> pdb=" O ARG E 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG E 220 " --> pdb=" O CYS E 233 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU E 235 " --> pdb=" O ASP E 218 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP E 218 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG E 237 " --> pdb=" O GLU E 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU E 216 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS E 239 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 224 through 225 Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 123 through 124 removed outlier: 8.069A pdb=" N CYS C 233 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG C 220 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU C 235 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP C 218 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG C 237 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU C 216 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS C 239 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB4, first strand: chain 'B' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.580A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 123 through 124 removed outlier: 8.070A pdb=" N CYS B 233 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG B 220 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU B 235 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP B 218 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ARG B 237 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU B 216 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS B 239 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB8, first strand: chain 'D' and resid 108 through 109 removed outlier: 4.309A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.581A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 removed outlier: 8.070A pdb=" N CYS D 233 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG D 220 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU D 235 " --> pdb=" O ASP D 218 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP D 218 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG D 237 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU D 216 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS D 239 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 865 hydrogen bonds defined for protein. 2550 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: 5.15 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2350 1.30 - 1.43: 4176 1.43 - 1.55: 8781 1.55 - 1.68: 87 1.68 - 1.81: 171 Bond restraints: 15565 Sorted by residual: bond pdb=" C43 IVM D 603 " pdb=" C44 IVM D 603 " ideal model delta sigma weight residual 1.330 1.682 -0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" C43 IVM E 901 " pdb=" C44 IVM E 901 " ideal model delta sigma weight residual 1.330 1.682 -0.352 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C43 IVM C 503 " pdb=" C44 IVM C 503 " ideal model delta sigma weight residual 1.330 1.681 -0.351 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C43 IVM A 604 " pdb=" C44 IVM A 604 " ideal model delta sigma weight residual 1.330 1.681 -0.351 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C43 IVM B 603 " pdb=" C44 IVM B 603 " ideal model delta sigma weight residual 1.330 1.681 -0.351 2.00e-02 2.50e+03 3.08e+02 ... (remaining 15560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.64: 20906 6.64 - 13.27: 159 13.27 - 19.91: 40 19.91 - 26.54: 5 26.54 - 33.18: 15 Bond angle restraints: 21125 Sorted by residual: angle pdb=" C7 IVM E 901 " pdb=" C6 IVM E 901 " pdb=" O14 IVM E 901 " ideal model delta sigma weight residual 106.56 73.38 33.18 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM C 503 " pdb=" C6 IVM C 503 " pdb=" O14 IVM C 503 " ideal model delta sigma weight residual 106.56 73.39 33.17 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM A 604 " pdb=" C6 IVM A 604 " pdb=" O14 IVM A 604 " ideal model delta sigma weight residual 106.56 73.39 33.17 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM B 603 " pdb=" C6 IVM B 603 " pdb=" O14 IVM B 603 " ideal model delta sigma weight residual 106.56 73.41 33.15 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C7 IVM D 603 " pdb=" C6 IVM D 603 " pdb=" O14 IVM D 603 " ideal model delta sigma weight residual 106.56 73.43 33.13 3.00e+00 1.11e-01 1.22e+02 ... (remaining 21120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 8712 22.48 - 44.97: 818 44.97 - 67.45: 185 67.45 - 89.93: 110 89.93 - 112.42: 95 Dihedral angle restraints: 9920 sinusoidal: 4580 harmonic: 5340 Sorted by residual: dihedral pdb=" C25 IVM B 603 " pdb=" C26 IVM B 603 " pdb=" C27 IVM B 603 " pdb=" C29 IVM B 603 " ideal model delta sinusoidal sigma weight residual 51.04 -61.38 112.42 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C25 IVM E 901 " pdb=" C26 IVM E 901 " pdb=" C27 IVM E 901 " pdb=" C29 IVM E 901 " ideal model delta sinusoidal sigma weight residual 51.04 -61.32 112.36 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C25 IVM C 503 " pdb=" C26 IVM C 503 " pdb=" C27 IVM C 503 " pdb=" C29 IVM C 503 " ideal model delta sinusoidal sigma weight residual 51.04 -61.30 112.34 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 9917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2290 0.146 - 0.292: 105 0.292 - 0.439: 25 0.439 - 0.585: 5 0.585 - 0.731: 5 Chirality restraints: 2430 Sorted by residual: chirality pdb=" C6 IVM D 603 " pdb=" C11 IVM D 603 " pdb=" C7 IVM D 603 " pdb=" O14 IVM D 603 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C6 IVM A 604 " pdb=" C11 IVM A 604 " pdb=" C7 IVM A 604 " pdb=" O14 IVM A 604 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C6 IVM C 503 " pdb=" C11 IVM C 503 " pdb=" C7 IVM C 503 " pdb=" O14 IVM C 503 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 2427 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C37 IVM A 604 " 0.412 2.00e-02 2.50e+03 3.83e-01 1.83e+03 pdb=" C38 IVM A 604 " -0.436 2.00e-02 2.50e+03 pdb=" C39 IVM A 604 " -0.408 2.00e-02 2.50e+03 pdb=" C40 IVM A 604 " -0.020 2.00e-02 2.50e+03 pdb=" C47 IVM A 604 " 0.452 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM D 603 " -0.412 2.00e-02 2.50e+03 3.82e-01 1.83e+03 pdb=" C38 IVM D 603 " 0.436 2.00e-02 2.50e+03 pdb=" C39 IVM D 603 " 0.408 2.00e-02 2.50e+03 pdb=" C40 IVM D 603 " 0.020 2.00e-02 2.50e+03 pdb=" C47 IVM D 603 " -0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM C 503 " -0.412 2.00e-02 2.50e+03 3.82e-01 1.83e+03 pdb=" C38 IVM C 503 " 0.436 2.00e-02 2.50e+03 pdb=" C39 IVM C 503 " 0.409 2.00e-02 2.50e+03 pdb=" C40 IVM C 503 " 0.019 2.00e-02 2.50e+03 pdb=" C47 IVM C 503 " -0.452 2.00e-02 2.50e+03 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3628 2.81 - 3.33: 14180 3.33 - 3.85: 25000 3.85 - 4.38: 28193 4.38 - 4.90: 50653 Nonbonded interactions: 121654 Sorted by model distance: nonbonded pdb=" OD1 ASN E 131 " pdb=" OG1 THR E 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN B 131 " pdb=" OG1 THR B 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN A 131 " pdb=" OG1 THR A 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN C 131 " pdb=" OG1 THR C 157 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASN D 131 " pdb=" OG1 THR D 157 " model vdw 2.283 3.040 ... (remaining 121649 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' and (resid 32 through 444 or resid 604)) selection = (chain 'B' and (resid 32 through 444 or resid 603)) selection = chain 'C' selection = (chain 'D' and (resid 32 through 444 or resid 603)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.530 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.017 0.352 15565 Z= 1.121 Angle : 1.854 33.178 21125 Z= 0.816 Chirality : 0.090 0.731 2430 Planarity : 0.027 0.383 2590 Dihedral : 23.000 112.416 6450 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.92 % Allowed : 11.04 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1785 helix: 2.04 (0.18), residues: 680 sheet: 1.54 (0.26), residues: 415 loop : -1.25 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 118 HIS 0.009 0.002 HIS E 133 PHE 0.029 0.004 PHE E 169 TYR 0.032 0.005 TYR A 433 ARG 0.009 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8469 (mmt) cc_final: 0.8195 (mmt) REVERT: B 42 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8138 (mmt) REVERT: D 42 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8018 (mmt) outliers start: 15 outliers final: 8 residues processed: 160 average time/residue: 0.2665 time to fit residues: 63.7726 Evaluate side-chains 124 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 70 ASN A 133 HIS E 62 ASN E 70 ASN E 133 HIS C 62 ASN C 70 ASN C 133 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 70 ASN B 133 HIS D 62 ASN D 70 ASN D 133 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15565 Z= 0.211 Angle : 0.810 10.047 21125 Z= 0.373 Chirality : 0.050 0.322 2430 Planarity : 0.004 0.031 2590 Dihedral : 18.458 106.934 2880 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.53 % Allowed : 12.52 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 1785 helix: 2.67 (0.18), residues: 730 sheet: 1.87 (0.26), residues: 410 loop : -1.27 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 118 HIS 0.002 0.001 HIS B 133 PHE 0.014 0.001 PHE C 422 TYR 0.026 0.002 TYR E 325 ARG 0.005 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.8378 (mmt) cc_final: 0.8087 (mmt) REVERT: E 113 MET cc_start: 0.8444 (ppp) cc_final: 0.7671 (ppp) REVERT: B 113 MET cc_start: 0.8512 (ppp) cc_final: 0.7610 (ppp) outliers start: 25 outliers final: 17 residues processed: 152 average time/residue: 0.3116 time to fit residues: 68.2662 Evaluate side-chains 132 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 0.0370 chunk 176 optimal weight: 7.9990 chunk 145 optimal weight: 0.0270 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15565 Z= 0.165 Angle : 0.710 10.955 21125 Z= 0.329 Chirality : 0.044 0.227 2430 Planarity : 0.003 0.027 2590 Dihedral : 13.675 83.409 2865 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.21 % Allowed : 13.68 % Favored : 84.11 % 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: 2.02 (0.20), residues: 1785 helix: 3.13 (0.18), residues: 690 sheet: 1.95 (0.26), residues: 415 loop : -1.09 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 263 HIS 0.001 0.000 HIS C 239 PHE 0.009 0.001 PHE C 422 TYR 0.023 0.002 TYR E 325 ARG 0.006 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8366 (ppp) cc_final: 0.8157 (ppp) REVERT: A 295 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7393 (mtm110) outliers start: 36 outliers final: 19 residues processed: 161 average time/residue: 0.2846 time to fit residues: 70.3473 Evaluate side-chains 142 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15565 Z= 0.429 Angle : 0.748 8.736 21125 Z= 0.373 Chirality : 0.047 0.241 2430 Planarity : 0.004 0.038 2590 Dihedral : 10.674 62.584 2865 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.94 % Allowed : 13.87 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 1785 helix: 2.64 (0.18), residues: 730 sheet: 1.95 (0.26), residues: 415 loop : -1.13 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 263 HIS 0.005 0.001 HIS E 133 PHE 0.017 0.002 PHE C 72 TYR 0.030 0.003 TYR E 325 ARG 0.005 0.001 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8426 (ppp) cc_final: 0.8102 (ppp) REVERT: C 315 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8979 (tt) outliers start: 48 outliers final: 31 residues processed: 159 average time/residue: 0.2612 time to fit residues: 62.8002 Evaluate side-chains 145 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.0020 chunk 129 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.1970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15565 Z= 0.200 Angle : 0.662 11.692 21125 Z= 0.320 Chirality : 0.044 0.215 2430 Planarity : 0.003 0.030 2590 Dihedral : 9.156 56.092 2865 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.76 % Allowed : 14.36 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.20), residues: 1785 helix: 3.14 (0.18), residues: 695 sheet: 1.88 (0.26), residues: 415 loop : -1.06 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 263 HIS 0.002 0.001 HIS E 133 PHE 0.011 0.001 PHE D 422 TYR 0.026 0.002 TYR E 325 ARG 0.005 0.000 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.8343 (ppp) cc_final: 0.7604 (ppp) REVERT: B 113 MET cc_start: 0.8509 (ppp) cc_final: 0.8263 (ppp) REVERT: B 315 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8968 (tt) REVERT: D 113 MET cc_start: 0.8467 (ppp) cc_final: 0.8187 (ppp) outliers start: 45 outliers final: 29 residues processed: 158 average time/residue: 0.2741 time to fit residues: 64.5698 Evaluate side-chains 148 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 0.3980 chunk 144 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15565 Z= 0.187 Angle : 0.627 10.173 21125 Z= 0.304 Chirality : 0.043 0.183 2430 Planarity : 0.003 0.035 2590 Dihedral : 8.075 57.343 2865 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.94 % Allowed : 14.60 % Favored : 82.45 % 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: 2.06 (0.20), residues: 1785 helix: 3.22 (0.18), residues: 695 sheet: 1.86 (0.26), residues: 415 loop : -1.10 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 263 HIS 0.002 0.000 HIS E 133 PHE 0.010 0.001 PHE B 422 TYR 0.024 0.002 TYR E 325 ARG 0.008 0.001 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 126 time to evaluate : 1.840 Fit side-chains revert: symmetry clash REVERT: C 315 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8854 (tt) REVERT: B 315 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8908 (tt) REVERT: D 187 MET cc_start: 0.8376 (tpt) cc_final: 0.8152 (tpt) outliers start: 48 outliers final: 30 residues processed: 158 average time/residue: 0.2651 time to fit residues: 63.3932 Evaluate side-chains 155 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 146 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15565 Z= 0.160 Angle : 0.619 10.285 21125 Z= 0.297 Chirality : 0.042 0.216 2430 Planarity : 0.003 0.026 2590 Dihedral : 7.506 56.804 2865 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.27 % Allowed : 15.21 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1785 helix: 3.33 (0.18), residues: 690 sheet: 1.85 (0.26), residues: 415 loop : -1.11 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 263 HIS 0.002 0.000 HIS A 335 PHE 0.010 0.001 PHE C 425 TYR 0.022 0.002 TYR E 325 ARG 0.005 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8237 (ppp) cc_final: 0.7428 (ppp) REVERT: D 187 MET cc_start: 0.8364 (tpt) cc_final: 0.8158 (tpt) outliers start: 37 outliers final: 26 residues processed: 166 average time/residue: 0.2573 time to fit residues: 64.5823 Evaluate side-chains 155 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15565 Z= 0.160 Angle : 0.613 13.930 21125 Z= 0.293 Chirality : 0.041 0.243 2430 Planarity : 0.003 0.043 2590 Dihedral : 7.092 57.069 2865 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 15.09 % Favored : 82.39 % 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: 2.08 (0.20), residues: 1785 helix: 3.34 (0.18), residues: 690 sheet: 1.80 (0.26), residues: 415 loop : -1.13 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 263 HIS 0.002 0.000 HIS D 239 PHE 0.009 0.001 PHE C 425 TYR 0.021 0.002 TYR E 325 ARG 0.008 0.000 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8306 (ppp) cc_final: 0.8051 (ppp) REVERT: C 315 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8775 (tt) outliers start: 41 outliers final: 30 residues processed: 170 average time/residue: 0.2517 time to fit residues: 65.8220 Evaluate side-chains 165 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 437 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15565 Z= 0.170 Angle : 0.617 13.105 21125 Z= 0.295 Chirality : 0.041 0.219 2430 Planarity : 0.003 0.034 2590 Dihedral : 6.823 56.686 2865 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.39 % Allowed : 15.34 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.20), residues: 1785 helix: 3.34 (0.18), residues: 690 sheet: 1.73 (0.26), residues: 415 loop : -1.13 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 263 HIS 0.002 0.000 HIS E 133 PHE 0.008 0.001 PHE C 425 TYR 0.022 0.002 TYR E 325 ARG 0.007 0.000 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8410 (ppp) cc_final: 0.8070 (ppp) REVERT: A 399 MET cc_start: 0.8384 (mmm) cc_final: 0.8142 (mmp) REVERT: E 113 MET cc_start: 0.8353 (ppp) cc_final: 0.7627 (ppp) REVERT: C 113 MET cc_start: 0.8270 (ppp) cc_final: 0.7631 (ppp) REVERT: C 287 MET cc_start: 0.8809 (tpp) cc_final: 0.8348 (tpt) REVERT: C 315 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8765 (tt) REVERT: D 113 MET cc_start: 0.8281 (ppp) cc_final: 0.7718 (ppp) outliers start: 39 outliers final: 34 residues processed: 166 average time/residue: 0.2603 time to fit residues: 65.9899 Evaluate side-chains 166 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 179 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.0270 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15565 Z= 0.196 Angle : 0.635 13.134 21125 Z= 0.304 Chirality : 0.042 0.227 2430 Planarity : 0.003 0.035 2590 Dihedral : 6.692 56.330 2865 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.58 % Allowed : 15.40 % Favored : 82.02 % 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: 2.01 (0.20), residues: 1785 helix: 3.32 (0.18), residues: 690 sheet: 1.69 (0.26), residues: 415 loop : -1.16 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 263 HIS 0.002 0.000 HIS E 133 PHE 0.008 0.001 PHE C 425 TYR 0.023 0.002 TYR E 325 ARG 0.007 0.000 ARG D 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8476 (ppp) cc_final: 0.8135 (ppp) REVERT: E 113 MET cc_start: 0.8369 (ppp) cc_final: 0.7787 (ppp) REVERT: C 287 MET cc_start: 0.8858 (tpp) cc_final: 0.8301 (tpt) REVERT: C 311 MET cc_start: 0.8103 (mmt) cc_final: 0.7746 (mmt) REVERT: C 315 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8801 (tt) REVERT: B 113 MET cc_start: 0.8334 (ppp) cc_final: 0.7406 (ppp) REVERT: D 113 MET cc_start: 0.8279 (ppp) cc_final: 0.7156 (ppp) outliers start: 42 outliers final: 35 residues processed: 166 average time/residue: 0.2591 time to fit residues: 65.5224 Evaluate side-chains 168 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0020 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 1.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065342 restraints weight = 35386.720| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.13 r_work: 0.2850 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15565 Z= 0.202 Angle : 0.632 12.082 21125 Z= 0.302 Chirality : 0.041 0.190 2430 Planarity : 0.003 0.029 2590 Dihedral : 6.616 56.021 2865 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.58 % Allowed : 15.28 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.20), residues: 1785 helix: 3.29 (0.18), residues: 695 sheet: 1.62 (0.26), residues: 415 loop : -1.12 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 263 HIS 0.002 0.000 HIS E 133 PHE 0.008 0.001 PHE C 425 TYR 0.023 0.002 TYR E 325 ARG 0.007 0.000 ARG D 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2783.07 seconds wall clock time: 50 minutes 50.01 seconds (3050.01 seconds total)