Starting phenix.real_space_refine on Thu Jun 12 18:51:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hin_0225/06_2025/6hin_0225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hin_0225/06_2025/6hin_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/cci-nas-00/data/ceres_data/6hin_0225/06_2025/6hin_0225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hin_0225/06_2025/6hin_0225.map" model { file = "/net/cci-nas-00/data/ceres_data/6hin_0225/06_2025/6hin_0225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hin_0225/06_2025/6hin_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.22, 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: 3.91 Conformation dependent library (CDL) restraints added in 1.8 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: 1.55 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: 3.73 Time building geometry restraints manager: 4.10 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: 0.880 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.120 Find NCS groups from input model: 0.780 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- 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 14650 Z= 0.429 Angle : 1.223 13.108 20080 Z= 0.609 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 15) link_NAG-ASN : angle 3.39824 ( 45) link_BETA1-4 : bond 0.00860 ( 10) link_BETA1-4 : angle 2.31315 ( 30) hydrogen bonds : bond 0.33225 ( 455) hydrogen bonds : angle 11.37438 ( 1320) SS BOND : bond 0.01080 ( 5) SS BOND : angle 1.55314 ( 10) covalent geometry : bond 0.00962 (14620) covalent geometry : angle 1.21109 (19995) *********************** 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 to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 1.464 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: 0.2725 time to fit residues: 108.2875 Evaluate side-chains 158 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101943 restraints weight = 29005.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102094 restraints weight = 21284.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102890 restraints weight = 15674.990| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 14650 Z= 0.184 Angle : 0.787 8.784 20080 Z= 0.404 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 15) link_NAG-ASN : angle 1.95965 ( 45) link_BETA1-4 : bond 0.00716 ( 10) link_BETA1-4 : angle 1.31638 ( 30) hydrogen bonds : bond 0.05372 ( 455) hydrogen bonds : angle 7.88894 ( 1320) SS BOND : bond 0.00426 ( 5) SS BOND : angle 0.48072 ( 10) covalent geometry : bond 0.00405 (14620) covalent geometry : angle 0.78105 (19995) *********************** 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 to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9277 (mt) cc_final: 0.8865 (mp) REVERT: A 94 TRP cc_start: 0.9410 (t60) cc_final: 0.8960 (t60) REVERT: A 130 GLN cc_start: 0.8286 (mt0) cc_final: 0.7666 (mp10) REVERT: A 184 GLN cc_start: 0.7604 (pm20) cc_final: 0.7365 (pm20) REVERT: A 197 LYS cc_start: 0.8497 (tptt) cc_final: 0.8289 (tmtt) REVERT: A 209 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 235 MET cc_start: 0.8530 (ttm) cc_final: 0.8163 (tpp) REVERT: A 291 MET cc_start: 0.8724 (mmp) cc_final: 0.7558 (mmm) REVERT: A 435 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8150 (tpt170) REVERT: A 436 LEU cc_start: 0.8519 (tt) cc_final: 0.8092 (pp) REVERT: A 448 TYR cc_start: 0.7695 (t80) cc_final: 0.7318 (t80) REVERT: B 74 GLN cc_start: 0.7664 (mt0) cc_final: 0.7368 (mt0) REVERT: B 209 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 235 MET cc_start: 0.8428 (ttm) cc_final: 0.7801 (tpp) REVERT: B 291 MET cc_start: 0.8626 (mmp) cc_final: 0.7874 (mmm) REVERT: B 435 ARG cc_start: 0.8443 (tpp-160) cc_final: 0.7991 (tpt170) REVERT: B 436 LEU cc_start: 0.8133 (tt) cc_final: 0.7785 (pp) REVERT: B 448 TYR cc_start: 0.7373 (t80) cc_final: 0.7111 (t80) REVERT: C 197 LYS cc_start: 0.8487 (tptt) cc_final: 0.8276 (tptt) REVERT: C 209 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 235 MET cc_start: 0.8602 (ttp) cc_final: 0.8111 (tpp) REVERT: C 255 LYS cc_start: 0.7884 (tttp) cc_final: 0.7518 (tttp) REVERT: C 291 MET cc_start: 0.8758 (mmp) cc_final: 0.7569 (mmm) REVERT: D 197 LYS cc_start: 0.8595 (tptt) cc_final: 0.8292 (tptt) REVERT: D 209 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7602 (tt0) REVERT: D 291 MET cc_start: 0.8866 (mmp) cc_final: 0.8127 (mmm) REVERT: D 436 LEU cc_start: 0.8130 (tt) cc_final: 0.7898 (pp) REVERT: D 448 TYR cc_start: 0.7708 (t80) cc_final: 0.7430 (t80) REVERT: E 209 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7587 (tt0) REVERT: E 235 MET cc_start: 0.8454 (ttm) cc_final: 0.8091 (tpp) REVERT: E 290 CYS cc_start: 0.7962 (t) cc_final: 0.7726 (p) REVERT: E 291 MET cc_start: 0.8740 (mmp) cc_final: 0.7438 (mmm) REVERT: E 436 LEU cc_start: 0.8315 (tt) cc_final: 0.7960 (pp) REVERT: E 448 TYR cc_start: 0.7520 (t80) cc_final: 0.7218 (t80) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3017 time to fit residues: 111.6692 Evaluate side-chains 173 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 0.2980 chunk 135 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103270 restraints weight = 29120.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104053 restraints weight = 25032.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105369 restraints weight = 18974.876| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14650 Z= 0.147 Angle : 0.725 8.514 20080 Z= 0.367 Chirality : 0.048 0.194 2400 Planarity : 0.004 0.032 2390 Dihedral : 7.310 38.986 2370 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 15) link_NAG-ASN : angle 1.92587 ( 45) link_BETA1-4 : bond 0.00485 ( 10) link_BETA1-4 : angle 1.19780 ( 30) hydrogen bonds : bond 0.04345 ( 455) hydrogen bonds : angle 7.02509 ( 1320) SS BOND : bond 0.00093 ( 5) SS BOND : angle 0.50725 ( 10) covalent geometry : bond 0.00334 (14620) covalent geometry : angle 0.71925 (19995) *********************** 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 251 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9261 (mt) cc_final: 0.8912 (mt) REVERT: A 209 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 291 MET cc_start: 0.8617 (mmp) cc_final: 0.8336 (mmm) REVERT: A 435 ARG cc_start: 0.8333 (tpp-160) cc_final: 0.8092 (tpt170) REVERT: A 436 LEU cc_start: 0.8449 (tt) cc_final: 0.8035 (pp) REVERT: A 452 LEU cc_start: 0.8822 (mt) cc_final: 0.7952 (tt) REVERT: B 130 GLN cc_start: 0.8251 (mt0) cc_final: 0.7789 (mp10) REVERT: B 209 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7455 (tt0) REVERT: B 210 MET cc_start: 0.8832 (tmm) cc_final: 0.8347 (tmm) REVERT: B 435 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7966 (tpt170) REVERT: B 436 LEU cc_start: 0.7976 (tt) cc_final: 0.7733 (pp) REVERT: C 197 LYS cc_start: 0.8241 (tptt) cc_final: 0.7980 (tptt) REVERT: C 209 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7616 (tm-30) REVERT: C 436 LEU cc_start: 0.8221 (tt) cc_final: 0.7847 (pp) REVERT: D 197 LYS cc_start: 0.8268 (tptt) cc_final: 0.8060 (tptt) REVERT: D 209 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7558 (tt0) REVERT: D 235 MET cc_start: 0.8536 (tpp) cc_final: 0.8319 (tpp) REVERT: D 291 MET cc_start: 0.8654 (mmp) cc_final: 0.8437 (mmm) REVERT: D 448 TYR cc_start: 0.7780 (t80) cc_final: 0.7578 (t80) REVERT: D 452 LEU cc_start: 0.8692 (mt) cc_final: 0.7688 (tt) REVERT: E 209 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7467 (tt0) REVERT: E 210 MET cc_start: 0.8572 (tmm) cc_final: 0.8103 (tmm) REVERT: E 291 MET cc_start: 0.8525 (mmp) cc_final: 0.8149 (mmm) REVERT: E 436 LEU cc_start: 0.8246 (tt) cc_final: 0.7981 (pp) REVERT: E 452 LEU cc_start: 0.8836 (mt) cc_final: 0.8034 (tt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2648 time to fit residues: 101.1244 Evaluate side-chains 169 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102497 restraints weight = 29113.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103052 restraints weight = 20971.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104380 restraints weight = 16161.166| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14650 Z= 0.150 Angle : 0.717 8.533 20080 Z= 0.357 Chirality : 0.047 0.250 2400 Planarity : 0.004 0.031 2390 Dihedral : 6.568 32.234 2370 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % 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: -2.27 (0.18), residues: 590 sheet: -2.10 (0.24), residues: 390 loop : -1.81 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 187 HIS 0.002 0.001 HIS D 158 PHE 0.038 0.002 PHE B 287 TYR 0.025 0.002 TYR C 67 ARG 0.003 0.000 ARG D 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 1.87372 ( 45) link_BETA1-4 : bond 0.00471 ( 10) link_BETA1-4 : angle 1.16699 ( 30) hydrogen bonds : bond 0.03846 ( 455) hydrogen bonds : angle 6.67666 ( 1320) SS BOND : bond 0.00293 ( 5) SS BOND : angle 0.21534 ( 10) covalent geometry : bond 0.00346 (14620) covalent geometry : angle 0.71107 (19995) *********************** 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 230 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8095 (tmtt) cc_final: 0.7679 (tmtt) REVERT: A 209 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 210 MET cc_start: 0.8663 (tmm) cc_final: 0.8272 (tmm) REVERT: A 291 MET cc_start: 0.8817 (mmp) cc_final: 0.8515 (mmm) REVERT: A 435 ARG cc_start: 0.8512 (tpp-160) cc_final: 0.8239 (tmt170) REVERT: A 436 LEU cc_start: 0.8407 (tt) cc_final: 0.8009 (pp) REVERT: A 448 TYR cc_start: 0.7860 (t80) cc_final: 0.7434 (t80) REVERT: B 197 LYS cc_start: 0.8159 (tptt) cc_final: 0.7895 (tmtt) REVERT: B 209 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7429 (tt0) REVERT: B 210 MET cc_start: 0.8800 (tmm) cc_final: 0.8519 (tmm) REVERT: B 238 ASP cc_start: 0.9086 (p0) cc_final: 0.8816 (p0) REVERT: B 435 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.7983 (tpt170) REVERT: C 197 LYS cc_start: 0.8126 (tptt) cc_final: 0.7867 (tptt) REVERT: C 209 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 266 LEU cc_start: 0.8580 (pp) cc_final: 0.8141 (tp) REVERT: C 436 LEU cc_start: 0.8095 (tt) cc_final: 0.7833 (pp) REVERT: D 57 VAL cc_start: 0.8755 (p) cc_final: 0.8547 (m) REVERT: D 209 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7593 (tt0) REVERT: D 291 MET cc_start: 0.8822 (mmp) cc_final: 0.8597 (mmm) REVERT: D 448 TYR cc_start: 0.7886 (t80) cc_final: 0.7399 (t80) REVERT: E 130 GLN cc_start: 0.8445 (mp10) cc_final: 0.8164 (mp10) REVERT: E 197 LYS cc_start: 0.8157 (tptt) cc_final: 0.7927 (tptt) REVERT: E 209 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7412 (tt0) REVERT: E 210 MET cc_start: 0.8647 (tmm) cc_final: 0.8159 (tmm) REVERT: E 266 LEU cc_start: 0.8607 (pp) cc_final: 0.8209 (tp) REVERT: E 291 MET cc_start: 0.8762 (mmp) cc_final: 0.8511 (mmm) REVERT: E 436 LEU cc_start: 0.8354 (tt) cc_final: 0.8041 (pp) REVERT: E 448 TYR cc_start: 0.7699 (t80) cc_final: 0.7458 (t80) REVERT: E 452 LEU cc_start: 0.8756 (mt) cc_final: 0.8082 (tt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2476 time to fit residues: 86.0699 Evaluate side-chains 164 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS C 158 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102912 restraints weight = 29379.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103728 restraints weight = 23532.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104989 restraints weight = 17206.977| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14650 Z= 0.157 Angle : 0.720 9.177 20080 Z= 0.358 Chirality : 0.047 0.172 2400 Planarity : 0.004 0.033 2390 Dihedral : 6.362 31.297 2370 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -3.03 (0.20), residues: 1655 helix: -1.99 (0.19), residues: 590 sheet: -2.08 (0.24), residues: 390 loop : -1.72 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 187 HIS 0.002 0.001 HIS D 158 PHE 0.036 0.002 PHE B 287 TYR 0.026 0.002 TYR B 286 ARG 0.005 0.001 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 1.83868 ( 45) link_BETA1-4 : bond 0.00485 ( 10) link_BETA1-4 : angle 1.18118 ( 30) hydrogen bonds : bond 0.03694 ( 455) hydrogen bonds : angle 6.49219 ( 1320) SS BOND : bond 0.01175 ( 5) SS BOND : angle 0.43463 ( 10) covalent geometry : bond 0.00365 (14620) covalent geometry : angle 0.71421 (19995) *********************** 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 241 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7681 (tmtt) REVERT: A 209 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 210 MET cc_start: 0.8641 (tmm) cc_final: 0.8216 (tmm) REVERT: A 291 MET cc_start: 0.8728 (mmp) cc_final: 0.8422 (mmm) REVERT: A 436 LEU cc_start: 0.8320 (tt) cc_final: 0.8053 (pp) REVERT: A 448 TYR cc_start: 0.8028 (t80) cc_final: 0.7366 (t80) REVERT: B 209 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7469 (tt0) REVERT: B 210 MET cc_start: 0.8835 (tmm) cc_final: 0.8479 (tmm) REVERT: B 255 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7843 (mtpt) REVERT: C 209 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7663 (tt0) REVERT: C 266 LEU cc_start: 0.8527 (pp) cc_final: 0.8082 (tp) REVERT: C 436 LEU cc_start: 0.8101 (tt) cc_final: 0.7881 (pp) REVERT: D 187 TRP cc_start: 0.8483 (m100) cc_final: 0.8134 (m100) REVERT: D 209 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7636 (tt0) REVERT: D 255 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7833 (mttm) REVERT: D 266 LEU cc_start: 0.8586 (pp) cc_final: 0.8201 (tp) REVERT: D 291 MET cc_start: 0.8638 (mmp) cc_final: 0.8430 (mmm) REVERT: D 298 LEU cc_start: 0.8659 (tp) cc_final: 0.8445 (tp) REVERT: D 448 TYR cc_start: 0.7612 (t80) cc_final: 0.7011 (t80) REVERT: E 209 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7364 (tt0) REVERT: E 210 MET cc_start: 0.8710 (tmm) cc_final: 0.8267 (tmm) REVERT: E 235 MET cc_start: 0.8098 (tpp) cc_final: 0.7844 (tpp) REVERT: E 266 LEU cc_start: 0.8526 (pp) cc_final: 0.8133 (tp) REVERT: E 436 LEU cc_start: 0.8199 (tt) cc_final: 0.7909 (pp) REVERT: E 448 TYR cc_start: 0.7791 (t80) cc_final: 0.7414 (t80) REVERT: E 452 LEU cc_start: 0.8797 (mt) cc_final: 0.8026 (tt) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3828 time to fit residues: 141.5752 Evaluate side-chains 167 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 136 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 149 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100663 restraints weight = 29350.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102911 restraints weight = 18566.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104378 restraints weight = 13465.134| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14650 Z= 0.141 Angle : 0.707 10.836 20080 Z= 0.350 Chirality : 0.047 0.423 2400 Planarity : 0.004 0.033 2390 Dihedral : 6.144 31.829 2370 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.20), residues: 1655 helix: -1.77 (0.20), residues: 595 sheet: -2.29 (0.24), residues: 380 loop : -1.69 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 187 HIS 0.010 0.001 HIS E 119 PHE 0.035 0.002 PHE E 287 TYR 0.031 0.002 TYR D 286 ARG 0.004 0.000 ARG E 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 15) link_NAG-ASN : angle 1.80052 ( 45) link_BETA1-4 : bond 0.00479 ( 10) link_BETA1-4 : angle 1.13882 ( 30) hydrogen bonds : bond 0.03443 ( 455) hydrogen bonds : angle 6.32147 ( 1320) SS BOND : bond 0.00154 ( 5) SS BOND : angle 0.24206 ( 10) covalent geometry : bond 0.00327 (14620) covalent geometry : angle 0.70239 (19995) *********************** 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 232 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7579 (tmtt) REVERT: A 209 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 210 MET cc_start: 0.8641 (tmm) cc_final: 0.7891 (tmm) REVERT: A 266 LEU cc_start: 0.8572 (pp) cc_final: 0.8289 (tp) REVERT: A 291 MET cc_start: 0.8946 (mmp) cc_final: 0.8716 (mmm) REVERT: A 436 LEU cc_start: 0.8316 (tt) cc_final: 0.8025 (pp) REVERT: A 448 TYR cc_start: 0.7756 (t80) cc_final: 0.7265 (t80) REVERT: B 120 ARG cc_start: 0.8613 (mmp-170) cc_final: 0.8371 (mmp-170) REVERT: B 197 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7741 (tptt) REVERT: B 209 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7425 (tt0) REVERT: C 197 LYS cc_start: 0.7980 (tmtt) cc_final: 0.7731 (tptt) REVERT: C 209 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7496 (tt0) REVERT: C 210 MET cc_start: 0.8574 (tmm) cc_final: 0.8227 (tmm) REVERT: C 266 LEU cc_start: 0.8459 (pp) cc_final: 0.8050 (tp) REVERT: C 436 LEU cc_start: 0.8049 (tt) cc_final: 0.7826 (pp) REVERT: D 209 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7601 (tt0) REVERT: D 210 MET cc_start: 0.8680 (tmm) cc_final: 0.8378 (tmm) REVERT: D 255 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7920 (mttm) REVERT: D 266 LEU cc_start: 0.8708 (pp) cc_final: 0.8337 (tp) REVERT: D 448 TYR cc_start: 0.7890 (t80) cc_final: 0.7274 (t80) REVERT: E 209 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7384 (tt0) REVERT: E 210 MET cc_start: 0.8709 (tmm) cc_final: 0.8298 (tmm) REVERT: E 266 LEU cc_start: 0.8646 (pp) cc_final: 0.8180 (tp) REVERT: E 436 LEU cc_start: 0.8200 (tt) cc_final: 0.7909 (pp) REVERT: E 452 LEU cc_start: 0.8678 (mt) cc_final: 0.8000 (tt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3853 time to fit residues: 134.9063 Evaluate side-chains 161 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 30 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS E 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098138 restraints weight = 29677.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100056 restraints weight = 19584.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101373 restraints weight = 14824.998| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14650 Z= 0.207 Angle : 0.773 10.285 20080 Z= 0.384 Chirality : 0.048 0.347 2400 Planarity : 0.004 0.036 2390 Dihedral : 6.268 31.598 2370 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -2.92 (0.20), residues: 1655 helix: -1.71 (0.20), residues: 595 sheet: -2.38 (0.24), residues: 380 loop : -1.63 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 68 HIS 0.013 0.001 HIS A 119 PHE 0.032 0.002 PHE B 287 TYR 0.018 0.002 TYR A 286 ARG 0.004 0.000 ARG E 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 15) link_NAG-ASN : angle 1.80227 ( 45) link_BETA1-4 : bond 0.00542 ( 10) link_BETA1-4 : angle 1.18317 ( 30) hydrogen bonds : bond 0.03678 ( 455) hydrogen bonds : angle 6.38295 ( 1320) SS BOND : bond 0.00996 ( 5) SS BOND : angle 0.57963 ( 10) covalent geometry : bond 0.00478 (14620) covalent geometry : angle 0.76854 (19995) *********************** 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 229 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8354 (tmtt) cc_final: 0.7950 (tmtt) REVERT: A 266 LEU cc_start: 0.8606 (pp) cc_final: 0.8291 (tp) REVERT: A 436 LEU cc_start: 0.8331 (tt) cc_final: 0.8023 (pp) REVERT: A 448 TYR cc_start: 0.8007 (t80) cc_final: 0.7425 (t80) REVERT: A 458 ILE cc_start: 0.7674 (mm) cc_final: 0.7459 (mm) REVERT: B 120 ARG cc_start: 0.8671 (mmp-170) cc_final: 0.8293 (mmp-170) REVERT: B 197 LYS cc_start: 0.8414 (tmtt) cc_final: 0.8058 (tptt) REVERT: B 209 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7639 (tt0) REVERT: B 210 MET cc_start: 0.8797 (tmm) cc_final: 0.8234 (tmm) REVERT: B 255 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8231 (mtpt) REVERT: B 266 LEU cc_start: 0.8665 (pp) cc_final: 0.8206 (tp) REVERT: C 197 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7513 (tptt) REVERT: C 209 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7590 (tm-30) REVERT: C 266 LEU cc_start: 0.8504 (pp) cc_final: 0.8086 (tp) REVERT: C 291 MET cc_start: 0.8383 (mmm) cc_final: 0.7855 (mmm) REVERT: C 436 LEU cc_start: 0.8083 (tt) cc_final: 0.7853 (pp) REVERT: D 124 GLN cc_start: 0.8277 (tt0) cc_final: 0.8004 (mt0) REVERT: D 209 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7798 (tt0) REVERT: D 210 MET cc_start: 0.8776 (tmm) cc_final: 0.8082 (tmm) REVERT: D 255 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7955 (mttm) REVERT: D 266 LEU cc_start: 0.8737 (pp) cc_final: 0.8294 (tp) REVERT: E 209 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7674 (tt0) REVERT: E 210 MET cc_start: 0.8777 (tmm) cc_final: 0.8336 (tmm) REVERT: E 266 LEU cc_start: 0.8668 (pp) cc_final: 0.8197 (tp) REVERT: E 436 LEU cc_start: 0.8177 (tt) cc_final: 0.7924 (pp) REVERT: E 452 LEU cc_start: 0.8787 (mt) cc_final: 0.8124 (tt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2409 time to fit residues: 83.5137 Evaluate side-chains 164 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101099 restraints weight = 29408.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103343 restraints weight = 18725.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104626 restraints weight = 13611.387| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14650 Z= 0.122 Angle : 0.707 8.711 20080 Z= 0.346 Chirality : 0.046 0.260 2400 Planarity : 0.004 0.033 2390 Dihedral : 6.019 31.316 2370 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -2.74 (0.21), residues: 1655 helix: -1.56 (0.21), residues: 595 sheet: -2.14 (0.24), residues: 390 loop : -1.60 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 156 HIS 0.002 0.000 HIS E 119 PHE 0.035 0.002 PHE E 287 TYR 0.032 0.002 TYR D 286 ARG 0.004 0.000 ARG D 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 15) link_NAG-ASN : angle 1.85897 ( 45) link_BETA1-4 : bond 0.00478 ( 10) link_BETA1-4 : angle 1.11609 ( 30) hydrogen bonds : bond 0.03183 ( 455) hydrogen bonds : angle 6.11943 ( 1320) SS BOND : bond 0.00527 ( 5) SS BOND : angle 0.13571 ( 10) covalent geometry : bond 0.00286 (14620) covalent geometry : angle 0.70129 (19995) *********************** 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 248 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7890 (mm110) cc_final: 0.7688 (mm110) REVERT: A 197 LYS cc_start: 0.8006 (tmtt) cc_final: 0.7275 (tmtt) REVERT: A 209 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 210 MET cc_start: 0.8615 (tmm) cc_final: 0.8114 (tmm) REVERT: A 233 PHE cc_start: 0.7455 (p90) cc_final: 0.7026 (m-10) REVERT: A 266 LEU cc_start: 0.8632 (pp) cc_final: 0.8278 (tp) REVERT: A 436 LEU cc_start: 0.8279 (tt) cc_final: 0.7995 (pp) REVERT: A 448 TYR cc_start: 0.8122 (t80) cc_final: 0.7485 (t80) REVERT: B 103 PHE cc_start: 0.8933 (p90) cc_final: 0.8704 (p90) REVERT: B 120 ARG cc_start: 0.8577 (mmp-170) cc_final: 0.8292 (mmp-170) REVERT: B 197 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7790 (tptt) REVERT: B 209 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7464 (tt0) REVERT: B 210 MET cc_start: 0.8770 (tmm) cc_final: 0.8232 (tmm) REVERT: B 266 LEU cc_start: 0.8657 (pp) cc_final: 0.8196 (tp) REVERT: B 291 MET cc_start: 0.7984 (mmm) cc_final: 0.7417 (mmm) REVERT: C 197 LYS cc_start: 0.8033 (tmtt) cc_final: 0.7712 (tptt) REVERT: C 210 MET cc_start: 0.8576 (tmm) cc_final: 0.8291 (tmm) REVERT: C 266 LEU cc_start: 0.8512 (pp) cc_final: 0.8077 (tp) REVERT: C 436 LEU cc_start: 0.8028 (tt) cc_final: 0.7794 (pp) REVERT: D 209 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7676 (tt0) REVERT: D 210 MET cc_start: 0.8648 (tmm) cc_final: 0.8388 (tmm) REVERT: D 266 LEU cc_start: 0.8674 (pp) cc_final: 0.8266 (tp) REVERT: D 448 TYR cc_start: 0.7912 (t80) cc_final: 0.7387 (t80) REVERT: E 209 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7474 (tt0) REVERT: E 210 MET cc_start: 0.8699 (tmm) cc_final: 0.8353 (tmm) REVERT: E 266 LEU cc_start: 0.8720 (pp) cc_final: 0.8241 (tp) REVERT: E 291 MET cc_start: 0.8311 (mmm) cc_final: 0.7569 (mmm) REVERT: E 436 LEU cc_start: 0.8134 (tt) cc_final: 0.7881 (pp) REVERT: E 448 TYR cc_start: 0.7719 (t80) cc_final: 0.7156 (t80) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3361 time to fit residues: 125.3543 Evaluate side-chains 175 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 136 optimal weight: 0.0470 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 10 optimal weight: 0.0060 chunk 162 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099515 restraints weight = 28865.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101682 restraints weight = 18421.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102950 restraints weight = 13511.458| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14650 Z= 0.151 Angle : 0.727 10.889 20080 Z= 0.357 Chirality : 0.046 0.226 2400 Planarity : 0.004 0.034 2390 Dihedral : 5.997 32.454 2370 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: -2.73 (0.21), residues: 1655 helix: -1.48 (0.21), residues: 595 sheet: -2.33 (0.23), residues: 380 loop : -1.54 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 187 HIS 0.002 0.001 HIS E 119 PHE 0.034 0.002 PHE B 287 TYR 0.024 0.002 TYR A 286 ARG 0.006 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 15) link_NAG-ASN : angle 1.79846 ( 45) link_BETA1-4 : bond 0.00445 ( 10) link_BETA1-4 : angle 1.12896 ( 30) hydrogen bonds : bond 0.03266 ( 455) hydrogen bonds : angle 6.10936 ( 1320) SS BOND : bond 0.00127 ( 5) SS BOND : angle 0.27812 ( 10) covalent geometry : bond 0.00352 (14620) covalent geometry : angle 0.72235 (19995) *********************** 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 231 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7487 (tptt) REVERT: A 209 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 210 MET cc_start: 0.8643 (tmm) cc_final: 0.8128 (tmm) REVERT: A 266 LEU cc_start: 0.8583 (pp) cc_final: 0.8296 (tp) REVERT: A 436 LEU cc_start: 0.8295 (tt) cc_final: 0.8011 (pp) REVERT: A 448 TYR cc_start: 0.8158 (t80) cc_final: 0.7510 (t80) REVERT: A 458 ILE cc_start: 0.7661 (mm) cc_final: 0.7440 (mm) REVERT: B 120 ARG cc_start: 0.8578 (mmp-170) cc_final: 0.8293 (mmp-170) REVERT: B 197 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7936 (tptt) REVERT: B 209 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7571 (tt0) REVERT: B 210 MET cc_start: 0.8777 (tmm) cc_final: 0.8223 (tmm) REVERT: B 266 LEU cc_start: 0.8691 (pp) cc_final: 0.8237 (tp) REVERT: B 290 CYS cc_start: 0.7784 (p) cc_final: 0.7317 (p) REVERT: B 291 MET cc_start: 0.8223 (mmm) cc_final: 0.7703 (mmm) REVERT: C 187 TRP cc_start: 0.8450 (m100) cc_final: 0.7956 (m100) REVERT: C 197 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7379 (tptt) REVERT: C 209 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 210 MET cc_start: 0.8562 (tmm) cc_final: 0.8116 (tmm) REVERT: C 266 LEU cc_start: 0.8516 (pp) cc_final: 0.8136 (tp) REVERT: C 291 MET cc_start: 0.8444 (mmt) cc_final: 0.7718 (mmm) REVERT: C 436 LEU cc_start: 0.8006 (tt) cc_final: 0.7788 (pp) REVERT: D 209 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7713 (tt0) REVERT: D 210 MET cc_start: 0.8667 (tmm) cc_final: 0.8048 (tmm) REVERT: D 266 LEU cc_start: 0.8680 (pp) cc_final: 0.8264 (tp) REVERT: E 103 PHE cc_start: 0.8890 (p90) cc_final: 0.8534 (p90) REVERT: E 209 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7612 (tt0) REVERT: E 210 MET cc_start: 0.8714 (tmm) cc_final: 0.8334 (tmm) REVERT: E 266 LEU cc_start: 0.8695 (pp) cc_final: 0.8221 (tp) REVERT: E 291 MET cc_start: 0.8427 (mmm) cc_final: 0.7707 (mmm) REVERT: E 436 LEU cc_start: 0.8038 (tt) cc_final: 0.7804 (pp) REVERT: E 448 TYR cc_start: 0.7788 (t80) cc_final: 0.7109 (t80) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2309 time to fit residues: 81.4524 Evaluate side-chains 161 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 0.0010 chunk 158 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100719 restraints weight = 29455.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101618 restraints weight = 20372.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102562 restraints weight = 15271.421| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14650 Z= 0.160 Angle : 0.744 10.996 20080 Z= 0.365 Chirality : 0.047 0.192 2400 Planarity : 0.004 0.037 2390 Dihedral : 6.001 32.301 2370 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.61 (0.21), residues: 1655 helix: -1.39 (0.21), residues: 595 sheet: -2.13 (0.23), residues: 390 loop : -1.54 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 156 HIS 0.002 0.001 HIS A 309 PHE 0.033 0.002 PHE E 287 TYR 0.033 0.002 TYR D 286 ARG 0.007 0.000 ARG D 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 15) link_NAG-ASN : angle 1.83691 ( 45) link_BETA1-4 : bond 0.00510 ( 10) link_BETA1-4 : angle 1.16727 ( 30) hydrogen bonds : bond 0.03291 ( 455) hydrogen bonds : angle 6.07199 ( 1320) SS BOND : bond 0.00072 ( 5) SS BOND : angle 0.31388 ( 10) covalent geometry : bond 0.00375 (14620) covalent geometry : angle 0.73911 (19995) ********************** 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 227 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8173 (tmtt) cc_final: 0.7530 (tptt) REVERT: A 209 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 266 LEU cc_start: 0.8569 (pp) cc_final: 0.8283 (tp) REVERT: A 436 LEU cc_start: 0.8284 (tt) cc_final: 0.7999 (pp) REVERT: A 448 TYR cc_start: 0.8139 (t80) cc_final: 0.7437 (t80) REVERT: B 120 ARG cc_start: 0.8588 (mmp-170) cc_final: 0.8313 (mmp-170) REVERT: B 197 LYS cc_start: 0.8314 (tmtt) cc_final: 0.7859 (tptt) REVERT: B 209 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 210 MET cc_start: 0.8793 (tmm) cc_final: 0.8384 (tmm) REVERT: B 255 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7981 (mttt) REVERT: B 290 CYS cc_start: 0.7650 (p) cc_final: 0.7103 (p) REVERT: B 291 MET cc_start: 0.8313 (mmm) cc_final: 0.7755 (mmm) REVERT: C 197 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7437 (tptt) REVERT: C 209 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 210 MET cc_start: 0.8578 (tmm) cc_final: 0.8131 (tmm) REVERT: C 266 LEU cc_start: 0.8488 (pp) cc_final: 0.8076 (tp) REVERT: C 291 MET cc_start: 0.8524 (mmt) cc_final: 0.7828 (mmm) REVERT: C 436 LEU cc_start: 0.8031 (tt) cc_final: 0.7772 (pp) REVERT: D 197 LYS cc_start: 0.8173 (tmtt) cc_final: 0.7304 (tptt) REVERT: D 209 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7335 (tm-30) REVERT: D 210 MET cc_start: 0.8668 (tmm) cc_final: 0.8109 (tmm) REVERT: D 266 LEU cc_start: 0.8679 (pp) cc_final: 0.8264 (tp) REVERT: D 291 MET cc_start: 0.8088 (mmt) cc_final: 0.7378 (mmm) REVERT: E 209 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7756 (tm-30) REVERT: E 210 MET cc_start: 0.8712 (tmm) cc_final: 0.8400 (tmm) REVERT: E 266 LEU cc_start: 0.8710 (pp) cc_final: 0.8257 (tp) REVERT: E 436 LEU cc_start: 0.8008 (tt) cc_final: 0.7766 (pp) REVERT: E 448 TYR cc_start: 0.7775 (t80) cc_final: 0.7257 (t80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2253 time to fit residues: 78.1300 Evaluate side-chains 159 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 21 optimal weight: 0.0050 chunk 42 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN E 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101831 restraints weight = 29363.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104033 restraints weight = 18485.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105303 restraints weight = 13473.195| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14650 Z= 0.120 Angle : 0.711 10.303 20080 Z= 0.346 Chirality : 0.046 0.166 2400 Planarity : 0.004 0.031 2390 Dihedral : 5.808 32.229 2370 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.21), residues: 1655 helix: -1.22 (0.21), residues: 590 sheet: -1.99 (0.24), residues: 380 loop : -1.60 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 156 HIS 0.002 0.000 HIS A 309 PHE 0.039 0.002 PHE B 287 TYR 0.017 0.002 TYR D 286 ARG 0.004 0.000 ARG D 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 15) link_NAG-ASN : angle 1.81847 ( 45) link_BETA1-4 : bond 0.00484 ( 10) link_BETA1-4 : angle 1.11085 ( 30) hydrogen bonds : bond 0.03050 ( 455) hydrogen bonds : angle 5.93369 ( 1320) SS BOND : bond 0.00082 ( 5) SS BOND : angle 0.15612 ( 10) covalent geometry : bond 0.00280 (14620) covalent geometry : angle 0.70644 (19995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4389.71 seconds wall clock time: 82 minutes 42.05 seconds (4962.05 seconds total)