Starting phenix.real_space_refine on Thu Sep 26 22:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hin_0225/09_2024/6hin_0225_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hin_0225/09_2024/6hin_0225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hin_0225/09_2024/6hin_0225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hin_0225/09_2024/6hin_0225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hin_0225/09_2024/6hin_0225_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hin_0225/09_2024/6hin_0225_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 40 5.16 5 C 9420 2.51 5 N 2220 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14220 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "B" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "C" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "D" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "E" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.20, per 1000 atoms: 0.65 Number of scatterers: 14220 At special positions: 0 Unit cell: (96.627, 96.627, 124.68, 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 40 16.00 O 2540 8.00 N 2220 7.00 C 9420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.02 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 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 501 " - " ASN D 82 " " NAG E 902 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN B 164 " " NAG I 1 " - " ASN B 148 " " NAG J 1 " - " ASN C 164 " " NAG K 1 " - " ASN C 148 " " NAG L 1 " - " ASN D 164 " " NAG M 1 " - " ASN D 148 " " NAG N 1 " - " ASN E 164 " " NAG O 1 " - " ASN E 148 " Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 2.0 seconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 15 sheets defined 38.5% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.736A pdb=" N LEU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 removed outlier: 3.868A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 250 through 271 removed outlier: 4.137A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.799A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.625A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.737A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.659A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.867A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 250 through 271 removed outlier: 4.137A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.798A pdb=" N PHE B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.625A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'C' and resid 11 through 20 removed outlier: 3.736A pdb=" N LEU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 removed outlier: 3.868A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 250 through 271 removed outlier: 4.136A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 261 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 269 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.798A pdb=" N PHE C 287 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 434 removed outlier: 3.624A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 442 " --> pdb=" O PHE C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 Processing helix chain 'D' and resid 11 through 20 removed outlier: 3.736A pdb=" N LEU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 removed outlier: 3.868A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 removed outlier: 3.653A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 250 through 271 removed outlier: 4.137A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU D 258 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.798A pdb=" N PHE D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.625A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.737A pdb=" N LEU E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 removed outlier: 3.867A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 241 Processing helix chain 'E' and resid 250 through 271 removed outlier: 4.136A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 258 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 264 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.799A pdb=" N PHE E 287 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 434 removed outlier: 3.624A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 446 removed outlier: 3.509A pdb=" N ILE E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 442 " --> pdb=" O PHE E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 133 removed outlier: 7.537A pdb=" N VAL A 57 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL A 51 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR A 59 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TRP A 63 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET A 45 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG A 65 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR A 67 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 41 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR A 69 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL A 39 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 3.533A pdb=" N LEU A 86 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.352A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU A 209 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 197 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 195 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 133 removed outlier: 7.537A pdb=" N VAL B 57 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL B 51 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR B 59 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP B 63 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET B 45 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG B 65 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL B 43 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR B 67 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE B 41 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 39 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 3.532A pdb=" N LEU B 86 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.352A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 197 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 195 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 133 removed outlier: 7.536A pdb=" N VAL C 57 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL C 51 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR C 59 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP C 63 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET C 45 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG C 65 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR C 67 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE C 41 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR C 69 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL C 39 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 3.532A pdb=" N LEU C 86 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.353A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 209 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 197 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C 195 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 122 through 133 removed outlier: 7.536A pdb=" N VAL D 57 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL D 51 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR D 59 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP D 63 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET D 45 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG D 65 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR D 67 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE D 41 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR D 69 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL D 39 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 removed outlier: 3.533A pdb=" N LEU D 86 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.353A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 197 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 195 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 122 through 133 removed outlier: 7.537A pdb=" N VAL E 57 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL E 51 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR E 59 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP E 63 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET E 45 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG E 65 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL E 43 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR E 67 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE E 41 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR E 69 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL E 39 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 removed outlier: 3.533A pdb=" N LEU E 86 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.352A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E 209 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 197 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1320 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: 3.67 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4142 1.34 - 1.45: 3065 1.45 - 1.57: 7353 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 14620 Sorted by residual: bond pdb=" CG SRO D 502 " pdb=" CD2 SRO D 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" CG SRO B 502 " pdb=" CD2 SRO B 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CG SRO C 502 " pdb=" CD2 SRO C 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CG SRO A 502 " pdb=" CD2 SRO A 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CG SRO E 901 " pdb=" CD2 SRO E 901 " ideal model delta sigma weight residual 1.438 1.356 0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 14615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 19244 2.62 - 5.24: 614 5.24 - 7.86: 87 7.86 - 10.49: 32 10.49 - 13.11: 18 Bond angle restraints: 19995 Sorted by residual: angle pdb=" CB SRO D 502 " pdb=" CG SRO D 502 " pdb=" CD1 SRO D 502 " ideal model delta sigma weight residual 128.15 115.04 13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CB SRO E 901 " pdb=" CG SRO E 901 " pdb=" CD1 SRO E 901 " ideal model delta sigma weight residual 128.15 115.08 13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CB SRO B 502 " pdb=" CG SRO B 502 " pdb=" CD1 SRO B 502 " ideal model delta sigma weight residual 128.15 115.11 13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CB SRO C 502 " pdb=" CG SRO C 502 " pdb=" CD1 SRO C 502 " ideal model delta sigma weight residual 128.15 115.11 13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CB SRO A 502 " pdb=" CG SRO A 502 " pdb=" CD1 SRO A 502 " ideal model delta sigma weight residual 128.15 115.11 13.04 3.00e+00 1.11e-01 1.89e+01 ... (remaining 19990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 8056 15.35 - 30.70: 624 30.70 - 46.05: 140 46.05 - 61.40: 25 61.40 - 76.75: 15 Dihedral angle restraints: 8860 sinusoidal: 3860 harmonic: 5000 Sorted by residual: dihedral pdb=" CA GLN E 66 " pdb=" C GLN E 66 " pdb=" N TYR E 67 " pdb=" CA TYR E 67 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLN C 66 " pdb=" C GLN C 66 " pdb=" N TYR C 67 " pdb=" CA TYR C 67 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLN D 66 " pdb=" C GLN D 66 " pdb=" N TYR D 67 " pdb=" CA TYR D 67 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 8857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1787 0.072 - 0.144: 533 0.144 - 0.215: 65 0.215 - 0.287: 10 0.287 - 0.359: 5 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CG LEU C 131 " pdb=" CB LEU C 131 " pdb=" CD1 LEU C 131 " pdb=" CD2 LEU C 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CG LEU D 131 " pdb=" CB LEU D 131 " pdb=" CD1 LEU D 131 " pdb=" CD2 LEU D 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU A 131 " pdb=" CB LEU A 131 " pdb=" CD1 LEU A 131 " pdb=" CD2 LEU A 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 2397 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " 0.017 2.00e-02 2.50e+03 1.72e-02 7.39e+00 pdb=" CG TRP C 168 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.017 2.00e-02 2.50e+03 1.70e-02 7.26e+00 pdb=" CG TRP B 168 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " -0.017 2.00e-02 2.50e+03 1.70e-02 7.26e+00 pdb=" CG TRP D 168 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " -0.002 2.00e-02 2.50e+03 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 5417 2.90 - 3.40: 14039 3.40 - 3.90: 23344 3.90 - 4.40: 25782 4.40 - 4.90: 42633 Nonbonded interactions: 111215 Sorted by model distance: nonbonded pdb=" N ASP C 52 " pdb=" OD1 ASP C 52 " model vdw 2.394 3.120 nonbonded pdb=" N ASP B 52 " pdb=" OD1 ASP B 52 " model vdw 2.394 3.120 nonbonded pdb=" N ASP E 52 " pdb=" OD1 ASP E 52 " model vdw 2.395 3.120 nonbonded pdb=" N ASP A 52 " pdb=" OD1 ASP A 52 " model vdw 2.395 3.120 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.395 3.120 ... (remaining 111210 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 10 through 459) selection = (chain 'B' and resid 10 through 459) selection = (chain 'C' and resid 10 through 459) selection = (chain 'D' and resid 10 through 459) selection = (chain 'E' and resid 10 through 459) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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 group one per residue 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: 0.730 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: 0.110 Set scattering table: 0.130 Process input model: 33.520 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.010 0.084 14620 Z= 0.618 Angle : 1.211 13.108 19995 Z= 0.607 Chirality : 0.067 0.359 2400 Planarity : 0.007 0.058 2390 Dihedral : 12.347 76.751 5595 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.32 % Allowed : 11.18 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.16), residues: 1655 helix: -4.58 (0.09), residues: 515 sheet: -2.32 (0.24), residues: 380 loop : -2.75 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP C 168 HIS 0.008 0.002 HIS B 119 PHE 0.023 0.003 PHE A 287 TYR 0.025 0.004 TYR B 116 ARG 0.008 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 TRP cc_start: 0.9357 (t60) cc_final: 0.8920 (t60) REVERT: A 197 LYS cc_start: 0.8828 (tptt) cc_final: 0.8609 (tmtt) REVERT: A 209 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 435 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.8008 (tpt170) REVERT: A 448 TYR cc_start: 0.7759 (t80) cc_final: 0.7554 (t80) REVERT: B 94 TRP cc_start: 0.9345 (t60) cc_final: 0.8904 (t60) REVERT: B 136 SER cc_start: 0.8760 (t) cc_final: 0.8381 (t) REVERT: B 209 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 290 CYS cc_start: 0.8523 (t) cc_final: 0.8006 (t) REVERT: B 435 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8113 (tpt170) REVERT: B 436 LEU cc_start: 0.8294 (tt) cc_final: 0.7898 (pp) REVERT: C 94 TRP cc_start: 0.9363 (t60) cc_final: 0.8866 (t60) REVERT: C 197 LYS cc_start: 0.8819 (tptt) cc_final: 0.8500 (tptt) REVERT: C 209 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 290 CYS cc_start: 0.8447 (t) cc_final: 0.7886 (t) REVERT: C 435 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8256 (tpt170) REVERT: D 94 TRP cc_start: 0.9369 (t60) cc_final: 0.8855 (t60) REVERT: D 197 LYS cc_start: 0.8825 (tptt) cc_final: 0.8432 (tptt) REVERT: D 209 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 435 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.8079 (tpt170) REVERT: D 436 LEU cc_start: 0.8132 (tt) cc_final: 0.7834 (pp) REVERT: D 448 TYR cc_start: 0.7714 (t80) cc_final: 0.7459 (t80) REVERT: E 94 TRP cc_start: 0.9384 (t60) cc_final: 0.8460 (t60) REVERT: E 197 LYS cc_start: 0.8925 (tptt) cc_final: 0.8651 (tptt) REVERT: E 435 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8372 (tpt170) REVERT: E 436 LEU cc_start: 0.8321 (tt) cc_final: 0.7894 (pp) outliers start: 5 outliers final: 0 residues processed: 274 average time/residue: 0.3105 time to fit residues: 122.1243 Evaluate side-chains 158 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 119 HIS C 101 ASN C 119 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 119 HIS E 101 ASN E 119 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14620 Z= 0.263 Angle : 0.781 8.784 19995 Z= 0.403 Chirality : 0.048 0.163 2400 Planarity : 0.005 0.039 2390 Dihedral : 8.744 53.519 2370 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: -4.09 (0.18), residues: 1655 helix: -3.35 (0.15), residues: 595 sheet: -2.08 (0.24), residues: 375 loop : -2.26 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 68 HIS 0.003 0.001 HIS D 158 PHE 0.039 0.002 PHE E 287 TYR 0.022 0.002 TYR B 67 ARG 0.005 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9284 (mt) cc_final: 0.8860 (mp) REVERT: A 94 TRP cc_start: 0.9425 (t60) cc_final: 0.8879 (t60) REVERT: A 130 GLN cc_start: 0.8284 (mt0) cc_final: 0.7634 (mp10) REVERT: A 184 GLN cc_start: 0.7610 (pm20) cc_final: 0.7361 (pm20) REVERT: A 197 LYS cc_start: 0.8489 (tptt) cc_final: 0.8166 (tmtt) REVERT: A 209 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 235 MET cc_start: 0.8599 (ttm) cc_final: 0.8167 (tpp) REVERT: A 291 MET cc_start: 0.8848 (mmp) cc_final: 0.7685 (mmm) REVERT: A 435 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8172 (tpt170) REVERT: A 436 LEU cc_start: 0.8500 (tt) cc_final: 0.8069 (pp) REVERT: A 448 TYR cc_start: 0.7707 (t80) cc_final: 0.7329 (t80) REVERT: B 74 GLN cc_start: 0.7747 (mt0) cc_final: 0.7498 (mt0) REVERT: B 209 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 235 MET cc_start: 0.8569 (ttm) cc_final: 0.7822 (tpp) REVERT: B 291 MET cc_start: 0.8815 (mmp) cc_final: 0.8025 (mmm) REVERT: B 435 ARG cc_start: 0.8488 (tpp-160) cc_final: 0.8011 (tpt170) REVERT: B 436 LEU cc_start: 0.8124 (tt) cc_final: 0.7767 (pp) REVERT: B 448 TYR cc_start: 0.7424 (t80) cc_final: 0.7169 (t80) REVERT: C 197 LYS cc_start: 0.8501 (tptt) cc_final: 0.8218 (tptt) REVERT: C 209 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 235 MET cc_start: 0.8682 (ttp) cc_final: 0.8104 (tpp) REVERT: C 255 LYS cc_start: 0.7955 (tttp) cc_final: 0.7571 (tttp) REVERT: C 291 MET cc_start: 0.8819 (mmp) cc_final: 0.7622 (mmm) REVERT: D 197 LYS cc_start: 0.8571 (tptt) cc_final: 0.8244 (tptt) REVERT: D 209 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7663 (tt0) REVERT: D 291 MET cc_start: 0.8909 (mmp) cc_final: 0.8155 (mmm) REVERT: D 436 LEU cc_start: 0.8132 (tt) cc_final: 0.7893 (pp) REVERT: D 448 TYR cc_start: 0.7707 (t80) cc_final: 0.7426 (t80) REVERT: E 209 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7618 (tt0) REVERT: E 235 MET cc_start: 0.8536 (ttm) cc_final: 0.8100 (tpp) REVERT: E 290 CYS cc_start: 0.8076 (t) cc_final: 0.7808 (p) REVERT: E 291 MET cc_start: 0.8817 (mmp) cc_final: 0.7529 (mmm) REVERT: E 436 LEU cc_start: 0.8302 (tt) cc_final: 0.7946 (pp) REVERT: E 448 TYR cc_start: 0.7522 (t80) cc_final: 0.7222 (t80) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2631 time to fit residues: 96.9464 Evaluate side-chains 173 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN D 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14620 Z= 0.220 Angle : 0.722 8.644 19995 Z= 0.367 Chirality : 0.048 0.199 2400 Planarity : 0.004 0.032 2390 Dihedral : 7.355 39.529 2370 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % 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: -3.55 (0.19), residues: 1655 helix: -2.64 (0.17), residues: 595 sheet: -2.01 (0.25), residues: 375 loop : -2.05 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 187 HIS 0.006 0.001 HIS D 119 PHE 0.033 0.002 PHE E 287 TYR 0.022 0.002 TYR D 286 ARG 0.004 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9273 (mt) cc_final: 0.8910 (mt) REVERT: A 120 ARG cc_start: 0.8085 (mmp-170) cc_final: 0.7839 (mmp-170) REVERT: A 184 GLN cc_start: 0.7671 (pm20) cc_final: 0.7312 (pm20) REVERT: A 197 LYS cc_start: 0.8154 (tptt) cc_final: 0.7896 (tmtt) REVERT: A 209 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 291 MET cc_start: 0.8909 (mmp) cc_final: 0.8655 (mmm) REVERT: A 435 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8172 (tpt170) REVERT: A 436 LEU cc_start: 0.8410 (tt) cc_final: 0.7981 (pp) REVERT: A 452 LEU cc_start: 0.8690 (mt) cc_final: 0.7934 (tt) REVERT: B 130 GLN cc_start: 0.8234 (mt0) cc_final: 0.7741 (mp10) REVERT: B 209 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7544 (tt0) REVERT: B 210 MET cc_start: 0.8908 (tmm) cc_final: 0.8363 (tmm) REVERT: B 435 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.8035 (tpt170) REVERT: B 436 LEU cc_start: 0.7989 (tt) cc_final: 0.7691 (pp) REVERT: C 197 LYS cc_start: 0.8245 (tptt) cc_final: 0.7903 (tptt) REVERT: C 209 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7514 (tm-30) REVERT: C 436 LEU cc_start: 0.8190 (tt) cc_final: 0.7802 (pp) REVERT: D 197 LYS cc_start: 0.8273 (tptt) cc_final: 0.8029 (tptt) REVERT: D 209 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7627 (tt0) REVERT: D 235 MET cc_start: 0.8711 (tpp) cc_final: 0.8474 (tpp) REVERT: D 291 MET cc_start: 0.8955 (mmp) cc_final: 0.8710 (mmm) REVERT: D 436 LEU cc_start: 0.8160 (tt) cc_final: 0.7897 (pp) REVERT: D 452 LEU cc_start: 0.8582 (mt) cc_final: 0.7729 (tt) REVERT: E 209 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7532 (tt0) REVERT: E 210 MET cc_start: 0.8657 (tmm) cc_final: 0.8107 (tmm) REVERT: E 235 MET cc_start: 0.8542 (ttm) cc_final: 0.8188 (tpp) REVERT: E 291 MET cc_start: 0.8849 (mmp) cc_final: 0.8531 (mmm) REVERT: E 436 LEU cc_start: 0.8249 (tt) cc_final: 0.7947 (pp) REVERT: E 452 LEU cc_start: 0.8736 (mt) cc_final: 0.8048 (tt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2511 time to fit residues: 93.1459 Evaluate side-chains 171 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.1980 chunk 112 optimal weight: 0.0060 chunk 77 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14620 Z= 0.176 Angle : 0.702 8.169 19995 Z= 0.347 Chirality : 0.047 0.242 2400 Planarity : 0.004 0.028 2390 Dihedral : 6.376 31.824 2370 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.20), residues: 1655 helix: -2.23 (0.18), residues: 585 sheet: -2.07 (0.24), residues: 405 loop : -1.85 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 187 HIS 0.002 0.001 HIS D 119 PHE 0.041 0.002 PHE B 287 TYR 0.026 0.002 TYR B 67 ARG 0.002 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9240 (mt) cc_final: 0.8892 (mt) REVERT: A 197 LYS cc_start: 0.7956 (tptt) cc_final: 0.7595 (tmtt) REVERT: A 209 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 210 MET cc_start: 0.8641 (tmm) cc_final: 0.8263 (tmm) REVERT: A 291 MET cc_start: 0.8968 (mmp) cc_final: 0.8663 (mmm) REVERT: A 435 ARG cc_start: 0.8618 (tpp-160) cc_final: 0.8099 (tpt170) REVERT: A 436 LEU cc_start: 0.8325 (tt) cc_final: 0.7937 (pp) REVERT: A 448 TYR cc_start: 0.7977 (t80) cc_final: 0.7460 (t80) REVERT: B 152 THR cc_start: 0.8844 (p) cc_final: 0.8415 (p) REVERT: B 209 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7421 (tt0) REVERT: B 210 MET cc_start: 0.8762 (tmm) cc_final: 0.8195 (tmm) REVERT: B 235 MET cc_start: 0.8072 (tpp) cc_final: 0.7651 (tpp) REVERT: B 435 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.8012 (tpt170) REVERT: C 152 THR cc_start: 0.8729 (p) cc_final: 0.8229 (p) REVERT: C 209 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7384 (tt0) REVERT: C 210 MET cc_start: 0.8585 (tmm) cc_final: 0.8164 (tmm) REVERT: C 266 LEU cc_start: 0.8550 (pp) cc_final: 0.8158 (tp) REVERT: C 436 LEU cc_start: 0.8071 (tt) cc_final: 0.7813 (pp) REVERT: D 197 LYS cc_start: 0.8051 (tptt) cc_final: 0.7811 (tptt) REVERT: D 209 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7464 (tt0) REVERT: D 291 MET cc_start: 0.8996 (mmp) cc_final: 0.8762 (mmm) REVERT: D 448 TYR cc_start: 0.7856 (t80) cc_final: 0.7422 (t80) REVERT: E 130 GLN cc_start: 0.8315 (mp10) cc_final: 0.8030 (mp10) REVERT: E 152 THR cc_start: 0.8688 (p) cc_final: 0.8280 (p) REVERT: E 197 LYS cc_start: 0.7832 (tptt) cc_final: 0.7520 (tmtt) REVERT: E 209 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7489 (tt0) REVERT: E 210 MET cc_start: 0.8631 (tmm) cc_final: 0.8120 (tmm) REVERT: E 235 MET cc_start: 0.8343 (ttm) cc_final: 0.8081 (tpp) REVERT: E 266 LEU cc_start: 0.8582 (pp) cc_final: 0.8222 (tp) REVERT: E 436 LEU cc_start: 0.8342 (tt) cc_final: 0.8020 (pp) REVERT: E 452 LEU cc_start: 0.8665 (mt) cc_final: 0.8011 (tt) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2436 time to fit residues: 93.1767 Evaluate side-chains 180 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.1980 chunk 90 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS B 158 HIS C 158 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14620 Z= 0.236 Angle : 0.714 9.195 19995 Z= 0.358 Chirality : 0.046 0.158 2400 Planarity : 0.004 0.031 2390 Dihedral : 6.177 31.514 2370 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: -3.03 (0.20), residues: 1655 helix: -1.92 (0.19), residues: 590 sheet: -2.21 (0.24), residues: 380 loop : -1.72 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 187 HIS 0.003 0.001 HIS B 119 PHE 0.034 0.002 PHE B 287 TYR 0.033 0.002 TYR D 286 ARG 0.005 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8351 (mm-40) REVERT: A 197 LYS cc_start: 0.8143 (tptt) cc_final: 0.7814 (tmtt) REVERT: A 209 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 210 MET cc_start: 0.8739 (tmm) cc_final: 0.8257 (tmm) REVERT: A 235 MET cc_start: 0.8467 (tpp) cc_final: 0.8184 (tpp) REVERT: A 266 LEU cc_start: 0.8517 (pp) cc_final: 0.8247 (tp) REVERT: A 291 MET cc_start: 0.9005 (mmp) cc_final: 0.8726 (mmm) REVERT: A 435 ARG cc_start: 0.8595 (tpp-160) cc_final: 0.8220 (tmt170) REVERT: A 436 LEU cc_start: 0.8336 (tt) cc_final: 0.7954 (pp) REVERT: A 448 TYR cc_start: 0.8063 (t80) cc_final: 0.7438 (t80) REVERT: B 197 LYS cc_start: 0.8029 (tptt) cc_final: 0.7544 (tmtt) REVERT: B 209 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7412 (tt0) REVERT: B 255 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8138 (mtpt) REVERT: B 435 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.7984 (tpt170) REVERT: C 120 ARG cc_start: 0.8511 (mmp-170) cc_final: 0.8251 (mmp-170) REVERT: C 209 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7597 (tt0) REVERT: C 210 MET cc_start: 0.8675 (tmm) cc_final: 0.8209 (tmm) REVERT: C 266 LEU cc_start: 0.8523 (pp) cc_final: 0.8151 (tp) REVERT: C 436 LEU cc_start: 0.8074 (tt) cc_final: 0.7818 (pp) REVERT: D 210 MET cc_start: 0.8715 (tmm) cc_final: 0.8384 (tmm) REVERT: D 291 MET cc_start: 0.9005 (mmp) cc_final: 0.8760 (mmm) REVERT: D 448 TYR cc_start: 0.7897 (t80) cc_final: 0.7217 (t80) REVERT: E 197 LYS cc_start: 0.8130 (tptt) cc_final: 0.7883 (tptt) REVERT: E 209 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7479 (tt0) REVERT: E 210 MET cc_start: 0.8733 (tmm) cc_final: 0.8175 (tmm) REVERT: E 235 MET cc_start: 0.8308 (ttm) cc_final: 0.8023 (tpp) REVERT: E 266 LEU cc_start: 0.8612 (pp) cc_final: 0.8204 (tp) REVERT: E 436 LEU cc_start: 0.8196 (tt) cc_final: 0.7884 (pp) REVERT: E 448 TYR cc_start: 0.7911 (t80) cc_final: 0.7622 (t80) REVERT: E 452 LEU cc_start: 0.8645 (mt) cc_final: 0.7977 (tt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2130 time to fit residues: 75.8912 Evaluate side-chains 164 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 14620 Z= 0.292 Angle : 0.735 12.026 19995 Z= 0.366 Chirality : 0.048 0.522 2400 Planarity : 0.004 0.033 2390 Dihedral : 6.195 31.872 2370 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % 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: -2.94 (0.20), residues: 1655 helix: -1.74 (0.20), residues: 595 sheet: -2.27 (0.24), residues: 380 loop : -1.71 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 187 HIS 0.009 0.001 HIS E 119 PHE 0.033 0.002 PHE E 287 TYR 0.015 0.002 TYR E 448 ARG 0.004 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8230 (mm-40) REVERT: A 197 LYS cc_start: 0.8204 (tptt) cc_final: 0.7926 (tmtt) REVERT: A 266 LEU cc_start: 0.8569 (pp) cc_final: 0.8279 (tp) REVERT: A 291 MET cc_start: 0.9046 (mmp) cc_final: 0.8788 (mmm) REVERT: A 435 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.8217 (tmt170) REVERT: A 436 LEU cc_start: 0.8282 (tt) cc_final: 0.7965 (pp) REVERT: A 448 TYR cc_start: 0.8078 (t80) cc_final: 0.7381 (t80) REVERT: B 197 LYS cc_start: 0.8186 (tptt) cc_final: 0.7681 (tmtt) REVERT: B 209 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7478 (tt0) REVERT: B 210 MET cc_start: 0.8815 (tmm) cc_final: 0.8170 (tmm) REVERT: B 235 MET cc_start: 0.8084 (tpp) cc_final: 0.7862 (tpp) REVERT: B 435 ARG cc_start: 0.8416 (tpp-160) cc_final: 0.7963 (tpt170) REVERT: C 120 ARG cc_start: 0.8518 (mmp-170) cc_final: 0.8280 (mmp-170) REVERT: C 195 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8379 (tm-30) REVERT: C 209 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7699 (tt0) REVERT: C 210 MET cc_start: 0.8718 (tmm) cc_final: 0.8289 (tmm) REVERT: C 266 LEU cc_start: 0.8504 (pp) cc_final: 0.8125 (tp) REVERT: C 436 LEU cc_start: 0.8056 (tt) cc_final: 0.7828 (pp) REVERT: D 75 TRP cc_start: 0.8028 (p90) cc_final: 0.7775 (p90) REVERT: D 197 LYS cc_start: 0.8380 (tmtt) cc_final: 0.8088 (tptt) REVERT: D 266 LEU cc_start: 0.8606 (pp) cc_final: 0.8279 (tp) REVERT: D 448 TYR cc_start: 0.7812 (t80) cc_final: 0.7175 (t80) REVERT: E 197 LYS cc_start: 0.8193 (tptt) cc_final: 0.7941 (tptt) REVERT: E 209 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7580 (tt0) REVERT: E 210 MET cc_start: 0.8804 (tmm) cc_final: 0.8311 (tmm) REVERT: E 266 LEU cc_start: 0.8603 (pp) cc_final: 0.8213 (tp) REVERT: E 436 LEU cc_start: 0.8123 (tt) cc_final: 0.7884 (pp) REVERT: E 452 LEU cc_start: 0.8681 (mt) cc_final: 0.8023 (tt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2442 time to fit residues: 82.4948 Evaluate side-chains 165 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14620 Z= 0.227 Angle : 0.722 10.159 19995 Z= 0.357 Chirality : 0.047 0.349 2400 Planarity : 0.004 0.036 2390 Dihedral : 6.109 32.146 2370 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -2.83 (0.20), residues: 1655 helix: -1.61 (0.20), residues: 595 sheet: -2.27 (0.24), residues: 380 loop : -1.64 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 187 HIS 0.003 0.001 HIS A 119 PHE 0.034 0.002 PHE E 287 TYR 0.029 0.002 TYR E 286 ARG 0.009 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8119 (tptt) cc_final: 0.7665 (tmtt) REVERT: A 209 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 210 MET cc_start: 0.8746 (tmm) cc_final: 0.8103 (tmm) REVERT: A 266 LEU cc_start: 0.8572 (pp) cc_final: 0.8280 (tp) REVERT: A 291 MET cc_start: 0.9025 (mmp) cc_final: 0.8757 (mmm) REVERT: A 435 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8211 (tmt170) REVERT: A 436 LEU cc_start: 0.8283 (tt) cc_final: 0.7968 (pp) REVERT: A 448 TYR cc_start: 0.7822 (t80) cc_final: 0.7272 (t80) REVERT: B 197 LYS cc_start: 0.8227 (tptt) cc_final: 0.7981 (tptt) REVERT: B 209 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7588 (tt0) REVERT: B 210 MET cc_start: 0.8842 (tmm) cc_final: 0.8195 (tmm) REVERT: B 266 LEU cc_start: 0.8678 (pp) cc_final: 0.8224 (tp) REVERT: B 435 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7903 (tpt170) REVERT: C 120 ARG cc_start: 0.8547 (mmp-170) cc_final: 0.8299 (mmp-170) REVERT: C 195 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8305 (tm-30) REVERT: C 209 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7706 (tt0) REVERT: C 210 MET cc_start: 0.8782 (tmm) cc_final: 0.8390 (tmm) REVERT: C 266 LEU cc_start: 0.8493 (pp) cc_final: 0.8076 (tp) REVERT: C 291 MET cc_start: 0.8394 (mmm) cc_final: 0.7849 (mmm) REVERT: C 436 LEU cc_start: 0.8052 (tt) cc_final: 0.7826 (pp) REVERT: D 75 TRP cc_start: 0.8163 (p90) cc_final: 0.7774 (p90) REVERT: D 187 TRP cc_start: 0.8301 (m100) cc_final: 0.8093 (m100) REVERT: D 197 LYS cc_start: 0.8274 (tmtt) cc_final: 0.8002 (tptt) REVERT: D 448 TYR cc_start: 0.7769 (t80) cc_final: 0.7197 (t80) REVERT: E 130 GLN cc_start: 0.8473 (mp10) cc_final: 0.8217 (mp10) REVERT: E 197 LYS cc_start: 0.8135 (tptt) cc_final: 0.7908 (tptt) REVERT: E 209 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7561 (tt0) REVERT: E 210 MET cc_start: 0.8766 (tmm) cc_final: 0.8295 (tmm) REVERT: E 266 LEU cc_start: 0.8626 (pp) cc_final: 0.8193 (tp) REVERT: E 436 LEU cc_start: 0.8096 (tt) cc_final: 0.7861 (pp) REVERT: E 448 TYR cc_start: 0.7972 (t80) cc_final: 0.7524 (t80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2511 time to fit residues: 89.0441 Evaluate side-chains 171 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 40.0000 chunk 144 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14620 Z= 0.223 Angle : 0.713 8.967 19995 Z= 0.353 Chirality : 0.047 0.270 2400 Planarity : 0.004 0.032 2390 Dihedral : 5.993 31.852 2370 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -2.76 (0.20), residues: 1655 helix: -1.51 (0.21), residues: 595 sheet: -2.29 (0.23), residues: 380 loop : -1.60 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 156 HIS 0.002 0.001 HIS A 119 PHE 0.034 0.002 PHE E 287 TYR 0.015 0.002 TYR A 286 ARG 0.003 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8080 (tptt) cc_final: 0.7670 (tmtt) REVERT: A 209 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 210 MET cc_start: 0.8755 (tmm) cc_final: 0.8112 (tmm) REVERT: A 266 LEU cc_start: 0.8591 (pp) cc_final: 0.8379 (tp) REVERT: A 291 MET cc_start: 0.9058 (mmp) cc_final: 0.8772 (mmm) REVERT: A 435 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.7989 (tpt170) REVERT: A 436 LEU cc_start: 0.8287 (tt) cc_final: 0.7965 (pp) REVERT: A 448 TYR cc_start: 0.7981 (t80) cc_final: 0.7466 (t80) REVERT: B 197 LYS cc_start: 0.8260 (tptt) cc_final: 0.8002 (tptt) REVERT: B 209 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7589 (tt0) REVERT: B 210 MET cc_start: 0.8821 (tmm) cc_final: 0.8171 (tmm) REVERT: B 255 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8105 (mtpt) REVERT: B 266 LEU cc_start: 0.8638 (pp) cc_final: 0.8196 (tp) REVERT: B 291 MET cc_start: 0.8126 (mmm) cc_final: 0.7519 (mmm) REVERT: B 435 ARG cc_start: 0.8120 (tpp-160) cc_final: 0.7874 (tpt170) REVERT: C 120 ARG cc_start: 0.8522 (mmp-170) cc_final: 0.8245 (mmp-170) REVERT: C 210 MET cc_start: 0.8770 (tmm) cc_final: 0.8399 (tmm) REVERT: C 266 LEU cc_start: 0.8528 (pp) cc_final: 0.8098 (tp) REVERT: C 436 LEU cc_start: 0.8034 (tt) cc_final: 0.7822 (pp) REVERT: D 197 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7907 (tptt) REVERT: D 255 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7803 (ptmt) REVERT: D 266 LEU cc_start: 0.8664 (pp) cc_final: 0.8257 (tp) REVERT: D 448 TYR cc_start: 0.7901 (t80) cc_final: 0.7366 (t80) REVERT: E 130 GLN cc_start: 0.8460 (mp10) cc_final: 0.8213 (mp10) REVERT: E 197 LYS cc_start: 0.8113 (tptt) cc_final: 0.7875 (tptt) REVERT: E 209 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7579 (tt0) REVERT: E 210 MET cc_start: 0.8734 (tmm) cc_final: 0.8281 (tmm) REVERT: E 233 PHE cc_start: 0.7733 (p90) cc_final: 0.7047 (m-10) REVERT: E 266 LEU cc_start: 0.8632 (pp) cc_final: 0.8198 (tp) REVERT: E 436 LEU cc_start: 0.8090 (tt) cc_final: 0.7843 (pp) REVERT: E 448 TYR cc_start: 0.7701 (t80) cc_final: 0.7368 (t80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2643 time to fit residues: 89.7410 Evaluate side-chains 160 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14620 Z= 0.194 Angle : 0.714 10.922 19995 Z= 0.349 Chirality : 0.046 0.225 2400 Planarity : 0.004 0.030 2390 Dihedral : 5.878 31.505 2370 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -2.58 (0.21), residues: 1655 helix: -1.41 (0.21), residues: 595 sheet: -2.00 (0.24), residues: 390 loop : -1.57 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 187 HIS 0.002 0.000 HIS C 309 PHE 0.035 0.002 PHE E 287 TYR 0.026 0.002 TYR D 286 ARG 0.003 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7924 (tptt) cc_final: 0.7506 (tmtt) REVERT: A 209 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7125 (tm-30) REVERT: A 210 MET cc_start: 0.8706 (tmm) cc_final: 0.8079 (tmm) REVERT: A 235 MET cc_start: 0.8330 (tpp) cc_final: 0.8128 (tpp) REVERT: A 266 LEU cc_start: 0.8542 (pp) cc_final: 0.8320 (tp) REVERT: A 291 MET cc_start: 0.9074 (mmp) cc_final: 0.8768 (mmm) REVERT: A 435 ARG cc_start: 0.8537 (tpp-160) cc_final: 0.7990 (tpt-90) REVERT: A 436 LEU cc_start: 0.8240 (tt) cc_final: 0.7970 (pp) REVERT: A 448 TYR cc_start: 0.8076 (t80) cc_final: 0.7503 (t80) REVERT: B 197 LYS cc_start: 0.8154 (tptt) cc_final: 0.7937 (tptt) REVERT: B 209 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7541 (tt0) REVERT: B 210 MET cc_start: 0.8710 (tmm) cc_final: 0.8075 (tmm) REVERT: B 255 LYS cc_start: 0.8332 (mtpt) cc_final: 0.8098 (mtpt) REVERT: B 266 LEU cc_start: 0.8658 (pp) cc_final: 0.8207 (tp) REVERT: B 291 MET cc_start: 0.8318 (mmm) cc_final: 0.7684 (mmm) REVERT: B 435 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7863 (tpt170) REVERT: C 120 ARG cc_start: 0.8505 (mmp-170) cc_final: 0.8216 (mmp-170) REVERT: C 187 TRP cc_start: 0.8449 (m100) cc_final: 0.7877 (m100) REVERT: C 266 LEU cc_start: 0.8426 (pp) cc_final: 0.8063 (tp) REVERT: C 291 MET cc_start: 0.8485 (mmt) cc_final: 0.7798 (mmm) REVERT: C 436 LEU cc_start: 0.8022 (tt) cc_final: 0.7755 (pp) REVERT: D 197 LYS cc_start: 0.8176 (tmtt) cc_final: 0.7867 (tptt) REVERT: D 255 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7789 (ptmt) REVERT: D 266 LEU cc_start: 0.8618 (pp) cc_final: 0.8205 (tp) REVERT: D 448 TYR cc_start: 0.7783 (t80) cc_final: 0.7058 (t80) REVERT: E 130 GLN cc_start: 0.8288 (mp10) cc_final: 0.8027 (mp10) REVERT: E 197 LYS cc_start: 0.8087 (tptt) cc_final: 0.7834 (tptt) REVERT: E 209 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7589 (tt0) REVERT: E 210 MET cc_start: 0.8717 (tmm) cc_final: 0.8319 (tmm) REVERT: E 233 PHE cc_start: 0.7639 (p90) cc_final: 0.7089 (m-10) REVERT: E 234 LEU cc_start: 0.8487 (pp) cc_final: 0.8240 (pp) REVERT: E 266 LEU cc_start: 0.8620 (pp) cc_final: 0.8172 (tp) REVERT: E 291 MET cc_start: 0.8251 (mmt) cc_final: 0.7436 (mmm) REVERT: E 436 LEU cc_start: 0.8031 (tt) cc_final: 0.7758 (pp) REVERT: E 448 TYR cc_start: 0.7795 (t80) cc_final: 0.7399 (t80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2480 time to fit residues: 85.3242 Evaluate side-chains 165 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 74 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 chunk 164 optimal weight: 0.0170 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14620 Z= 0.186 Angle : 0.702 10.380 19995 Z= 0.342 Chirality : 0.046 0.183 2400 Planarity : 0.004 0.030 2390 Dihedral : 5.732 31.718 2370 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -2.48 (0.21), residues: 1655 helix: -1.23 (0.21), residues: 590 sheet: -1.94 (0.24), residues: 390 loop : -1.61 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 187 HIS 0.002 0.000 HIS D 119 PHE 0.033 0.002 PHE E 287 TYR 0.024 0.002 TYR B 286 ARG 0.003 0.000 ARG E 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7863 (tptt) cc_final: 0.7448 (tmtt) REVERT: A 209 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7075 (tm-30) REVERT: A 210 MET cc_start: 0.8601 (tmm) cc_final: 0.8080 (tmm) REVERT: A 266 LEU cc_start: 0.8522 (pp) cc_final: 0.8303 (tp) REVERT: A 291 MET cc_start: 0.9059 (mmp) cc_final: 0.8741 (mmm) REVERT: A 435 ARG cc_start: 0.8523 (tpp-160) cc_final: 0.8025 (tpt170) REVERT: A 436 LEU cc_start: 0.8245 (tt) cc_final: 0.7964 (pp) REVERT: A 448 TYR cc_start: 0.8089 (t80) cc_final: 0.7422 (t80) REVERT: B 120 ARG cc_start: 0.8555 (mmp-170) cc_final: 0.8338 (mmp-170) REVERT: B 197 LYS cc_start: 0.8099 (tptt) cc_final: 0.7862 (tptt) REVERT: B 209 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7537 (tt0) REVERT: B 210 MET cc_start: 0.8707 (tmm) cc_final: 0.8127 (tmm) REVERT: B 255 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8089 (mtpt) REVERT: B 291 MET cc_start: 0.8368 (mmm) cc_final: 0.7672 (mmm) REVERT: B 435 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7810 (tpt170) REVERT: C 120 ARG cc_start: 0.8458 (mmp-170) cc_final: 0.8176 (mmp-170) REVERT: C 266 LEU cc_start: 0.8493 (pp) cc_final: 0.8066 (tp) REVERT: C 436 LEU cc_start: 0.8004 (tt) cc_final: 0.7747 (pp) REVERT: D 152 THR cc_start: 0.8807 (p) cc_final: 0.8306 (p) REVERT: D 197 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7769 (tptt) REVERT: D 255 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7781 (ptmt) REVERT: D 266 LEU cc_start: 0.8529 (pp) cc_final: 0.8141 (tp) REVERT: D 448 TYR cc_start: 0.7728 (t80) cc_final: 0.7038 (t80) REVERT: E 130 GLN cc_start: 0.8343 (mp10) cc_final: 0.8102 (mp10) REVERT: E 136 SER cc_start: 0.9098 (m) cc_final: 0.8870 (t) REVERT: E 197 LYS cc_start: 0.7946 (tptt) cc_final: 0.7598 (tptt) REVERT: E 209 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7548 (tt0) REVERT: E 210 MET cc_start: 0.8696 (tmm) cc_final: 0.8320 (tmm) REVERT: E 233 PHE cc_start: 0.7595 (p90) cc_final: 0.7072 (m-10) REVERT: E 234 LEU cc_start: 0.8533 (pp) cc_final: 0.8281 (pp) REVERT: E 266 LEU cc_start: 0.8635 (pp) cc_final: 0.8173 (tp) REVERT: E 290 CYS cc_start: 0.7701 (p) cc_final: 0.6838 (p) REVERT: E 291 MET cc_start: 0.8155 (mmt) cc_final: 0.7565 (mmm) REVERT: E 436 LEU cc_start: 0.7939 (tt) cc_final: 0.7685 (pp) REVERT: E 448 TYR cc_start: 0.7949 (t80) cc_final: 0.7444 (t80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2496 time to fit residues: 87.4527 Evaluate side-chains 171 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101141 restraints weight = 29320.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102215 restraints weight = 19560.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103095 restraints weight = 15481.720| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14620 Z= 0.254 Angle : 0.734 10.229 19995 Z= 0.362 Chirality : 0.046 0.167 2400 Planarity : 0.004 0.032 2390 Dihedral : 5.839 31.776 2370 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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 (0.21), residues: 1655 helix: -1.22 (0.21), residues: 595 sheet: -2.19 (0.23), residues: 380 loop : -1.53 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 187 HIS 0.001 0.001 HIS E 119 PHE 0.037 0.002 PHE B 287 TYR 0.023 0.002 TYR D 286 ARG 0.004 0.000 ARG E 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2762.56 seconds wall clock time: 52 minutes 5.61 seconds (3125.61 seconds total)