Starting phenix.real_space_refine on Fri Jan 17 00:26:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0d_45080/01_2025/9c0d_45080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0d_45080/01_2025/9c0d_45080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0d_45080/01_2025/9c0d_45080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0d_45080/01_2025/9c0d_45080.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0d_45080/01_2025/9c0d_45080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0d_45080/01_2025/9c0d_45080.cif" } resolution = 3.97 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= 0.014 sd= 0.053 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 140 5.16 5 C 33992 2.51 5 N 9268 2.21 5 O 11130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 54530 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "B" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "C" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "I" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "D" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "J" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "E" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "K" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "F" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "L" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "G" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "M" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "H" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Chain: "N" Number of atoms: 3895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3895 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 12, 'TRANS': 511} Time building chain proxies: 24.00, per 1000 atoms: 0.44 Number of scatterers: 54530 At special positions: 0 Unit cell: (161, 163.3, 166.75, 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 140 16.00 O 11130 8.00 N 9268 7.00 C 33992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 5.9 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13440 Finding SS restraints... Secondary structure from input PDB file: 343 helices and 91 sheets defined 60.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.841A pdb=" N ARG A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.566A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 108 removed outlier: 3.765A pdb=" N THR A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 154 through 168 removed outlier: 3.965A pdb=" N HIS A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.917A pdb=" N MET A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.126A pdb=" N LYS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'A' and resid 356 through 373 removed outlier: 4.236A pdb=" N GLY A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 407 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.531A pdb=" N THR A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.778A pdb=" N ARG B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 63 through 82 removed outlier: 3.575A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 108 removed outlier: 3.807A pdb=" N THR B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 133 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 154 through 168 removed outlier: 4.110A pdb=" N HIS B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.935A pdb=" N MET B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.117A pdb=" N LYS B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 336 through 354 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 383 through 407 Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 430 through 444 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 494 through 513 Processing helix chain 'C' and resid 8 through 27 removed outlier: 3.745A pdb=" N ARG C 12 " --> pdb=" O ALA C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 63 through 82 removed outlier: 3.585A pdb=" N LYS C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 108 removed outlier: 3.784A pdb=" N THR C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 133 Processing helix chain 'C' and resid 139 through 151 removed outlier: 4.327A pdb=" N SER C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 168 removed outlier: 3.806A pdb=" N HIS C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.913A pdb=" N MET C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 255 through 266 Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.012A pdb=" N LYS C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 336 through 354 Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 383 through 407 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 430 through 444 Processing helix chain 'C' and resid 445 through 455 Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.569A pdb=" N ASN C 468 " --> pdb=" O ASP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 494 through 513 Processing helix chain 'I' and resid 8 through 27 removed outlier: 3.698A pdb=" N ARG I 12 " --> pdb=" O ALA I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 51 through 59 removed outlier: 3.501A pdb=" N ILE I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 82 removed outlier: 3.965A pdb=" N LYS I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR I 80 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP I 82 " --> pdb=" O SER I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 108 removed outlier: 3.797A pdb=" N THR I 90 " --> pdb=" O ASP I 86 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 91 " --> pdb=" O GLY I 87 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR I 92 " --> pdb=" O THR I 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 133 Processing helix chain 'I' and resid 139 through 148 Processing helix chain 'I' and resid 154 through 168 removed outlier: 4.025A pdb=" N HIS I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 203 removed outlier: 3.972A pdb=" N MET I 202 " --> pdb=" O SER I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 230 Processing helix chain 'I' and resid 231 through 242 Processing helix chain 'I' and resid 255 through 266 Processing helix chain 'I' and resid 280 through 295 removed outlier: 4.084A pdb=" N LYS I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET I 286 " --> pdb=" O ARG I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'I' and resid 336 through 354 Processing helix chain 'I' and resid 356 through 372 Processing helix chain 'I' and resid 383 through 407 Processing helix chain 'I' and resid 414 through 420 Processing helix chain 'I' and resid 420 through 426 Processing helix chain 'I' and resid 430 through 444 Processing helix chain 'I' and resid 445 through 455 Processing helix chain 'I' and resid 458 through 467 Processing helix chain 'I' and resid 484 through 489 Processing helix chain 'I' and resid 494 through 513 Processing helix chain 'D' and resid 8 through 27 removed outlier: 3.897A pdb=" N ARG D 12 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.526A pdb=" N LYS D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 108 removed outlier: 3.704A pdb=" N THR D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 133 removed outlier: 3.676A pdb=" N ILE D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 154 through 167 removed outlier: 4.086A pdb=" N HIS D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 removed outlier: 4.000A pdb=" N MET D 202 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 280 through 295 removed outlier: 4.135A pdb=" N LYS D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET D 286 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 336 through 354 Processing helix chain 'D' and resid 356 through 372 Processing helix chain 'D' and resid 383 through 407 Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 430 through 444 Processing helix chain 'D' and resid 445 through 455 Processing helix chain 'D' and resid 458 through 467 Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 494 through 513 Processing helix chain 'J' and resid 8 through 28 removed outlier: 3.811A pdb=" N ARG J 12 " --> pdb=" O ALA J 8 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 59 Processing helix chain 'J' and resid 63 through 81 removed outlier: 3.608A pdb=" N LYS J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR J 80 " --> pdb=" O VAL J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 108 removed outlier: 3.870A pdb=" N THR J 90 " --> pdb=" O ASP J 86 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR J 92 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA J 108 " --> pdb=" O LYS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 133 removed outlier: 3.742A pdb=" N ILE J 115 " --> pdb=" O ASN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 154 through 168 removed outlier: 3.942A pdb=" N HIS J 158 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.919A pdb=" N MET J 202 " --> pdb=" O SER J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 230 Processing helix chain 'J' and resid 231 through 242 Processing helix chain 'J' and resid 255 through 266 Processing helix chain 'J' and resid 279 through 295 removed outlier: 4.055A pdb=" N LYS J 284 " --> pdb=" O GLY J 280 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA J 285 " --> pdb=" O ASP J 281 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET J 286 " --> pdb=" O ARG J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 304 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 336 through 354 Processing helix chain 'J' and resid 356 through 372 Processing helix chain 'J' and resid 383 through 407 Processing helix chain 'J' and resid 414 through 420 Processing helix chain 'J' and resid 420 through 426 Processing helix chain 'J' and resid 430 through 444 Processing helix chain 'J' and resid 445 through 455 Processing helix chain 'J' and resid 458 through 467 Processing helix chain 'J' and resid 484 through 489 Processing helix chain 'J' and resid 494 through 513 Processing helix chain 'E' and resid 8 through 27 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 51 through 59 Processing helix chain 'E' and resid 63 through 82 removed outlier: 3.563A pdb=" N LYS E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 80 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 107 removed outlier: 3.726A pdb=" N THR E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA E 91 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 133 removed outlier: 3.706A pdb=" N ILE E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 154 through 168 removed outlier: 3.867A pdb=" N HIS E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.926A pdb=" N MET E 202 " --> pdb=" O SER E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 231 through 242 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'E' and resid 280 through 295 removed outlier: 4.093A pdb=" N LYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET E 286 " --> pdb=" O ARG E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 336 through 354 Processing helix chain 'E' and resid 356 through 372 Processing helix chain 'E' and resid 383 through 407 Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'E' and resid 420 through 426 Processing helix chain 'E' and resid 430 through 444 Processing helix chain 'E' and resid 445 through 455 Processing helix chain 'E' and resid 458 through 467 Processing helix chain 'E' and resid 484 through 489 Processing helix chain 'E' and resid 494 through 513 Processing helix chain 'K' and resid 8 through 27 removed outlier: 3.959A pdb=" N ARG K 12 " --> pdb=" O ALA K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 51 through 59 Processing helix chain 'K' and resid 63 through 82 removed outlier: 3.643A pdb=" N LYS K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR K 80 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP K 82 " --> pdb=" O SER K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 108 removed outlier: 3.821A pdb=" N THR K 90 " --> pdb=" O ASP K 86 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA K 91 " --> pdb=" O GLY K 87 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 133 Processing helix chain 'K' and resid 139 through 148 Processing helix chain 'K' and resid 154 through 168 removed outlier: 3.995A pdb=" N HIS K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 203 removed outlier: 3.977A pdb=" N MET K 202 " --> pdb=" O SER K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 230 Processing helix chain 'K' and resid 231 through 242 Processing helix chain 'K' and resid 255 through 266 Processing helix chain 'K' and resid 279 through 295 removed outlier: 4.000A pdb=" N LYS K 284 " --> pdb=" O GLY K 280 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA K 285 " --> pdb=" O ASP K 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET K 286 " --> pdb=" O ARG K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 336 through 354 Processing helix chain 'K' and resid 356 through 372 Processing helix chain 'K' and resid 383 through 407 Processing helix chain 'K' and resid 414 through 420 Processing helix chain 'K' and resid 420 through 426 Processing helix chain 'K' and resid 430 through 444 Processing helix chain 'K' and resid 445 through 455 Processing helix chain 'K' and resid 458 through 467 Processing helix chain 'K' and resid 484 through 489 Processing helix chain 'K' and resid 494 through 513 removed outlier: 3.550A pdb=" N THR K 513 " --> pdb=" O ALA K 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 28 removed outlier: 3.722A pdb=" N ARG F 12 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 59 Processing helix chain 'F' and resid 63 through 82 removed outlier: 3.600A pdb=" N LYS F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR F 80 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 108 removed outlier: 3.850A pdb=" N THR F 90 " --> pdb=" O ASP F 86 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR F 92 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 133 removed outlier: 3.755A pdb=" N ILE F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'F' and resid 154 through 168 removed outlier: 3.980A pdb=" N HIS F 158 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.893A pdb=" N MET F 202 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 280 through 295 removed outlier: 4.123A pdb=" N LYS F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 285 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET F 286 " --> pdb=" O ARG F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 354 Processing helix chain 'F' and resid 356 through 372 Processing helix chain 'F' and resid 383 through 407 Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'F' and resid 420 through 426 Processing helix chain 'F' and resid 430 through 444 Processing helix chain 'F' and resid 445 through 455 Processing helix chain 'F' and resid 458 through 467 Processing helix chain 'F' and resid 484 through 489 Processing helix chain 'F' and resid 494 through 513 Processing helix chain 'L' and resid 8 through 27 removed outlier: 4.065A pdb=" N ARG L 12 " --> pdb=" O ALA L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 30 No H-bonds generated for 'chain 'L' and resid 28 through 30' Processing helix chain 'L' and resid 51 through 59 Processing helix chain 'L' and resid 63 through 82 removed outlier: 3.574A pdb=" N LYS L 79 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR L 80 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP L 82 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 108 removed outlier: 3.785A pdb=" N THR L 90 " --> pdb=" O ASP L 86 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA L 91 " --> pdb=" O GLY L 87 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR L 92 " --> pdb=" O THR L 88 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA L 108 " --> pdb=" O LYS L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 133 Processing helix chain 'L' and resid 139 through 148 Processing helix chain 'L' and resid 154 through 168 removed outlier: 3.990A pdb=" N HIS L 158 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 203 removed outlier: 3.991A pdb=" N MET L 202 " --> pdb=" O SER L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 230 Processing helix chain 'L' and resid 231 through 242 Processing helix chain 'L' and resid 255 through 266 Processing helix chain 'L' and resid 280 through 295 removed outlier: 4.150A pdb=" N LYS L 284 " --> pdb=" O GLY L 280 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA L 285 " --> pdb=" O ASP L 281 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET L 286 " --> pdb=" O ARG L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 304 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 336 through 354 Processing helix chain 'L' and resid 356 through 372 Processing helix chain 'L' and resid 383 through 407 Processing helix chain 'L' and resid 414 through 420 Processing helix chain 'L' and resid 420 through 426 Processing helix chain 'L' and resid 430 through 444 Processing helix chain 'L' and resid 445 through 455 Processing helix chain 'L' and resid 458 through 467 Processing helix chain 'L' and resid 484 through 489 Processing helix chain 'L' and resid 494 through 513 Processing helix chain 'G' and resid 8 through 27 removed outlier: 4.146A pdb=" N ARG G 12 " --> pdb=" O ALA G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 51 through 59 Processing helix chain 'G' and resid 63 through 81 removed outlier: 3.558A pdb=" N LYS G 79 " --> pdb=" O GLU G 75 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 108 removed outlier: 3.747A pdb=" N THR G 90 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR G 92 " --> pdb=" O THR G 88 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 133 Processing helix chain 'G' and resid 139 through 148 Processing helix chain 'G' and resid 154 through 168 removed outlier: 4.060A pdb=" N HIS G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 203 removed outlier: 3.852A pdb=" N MET G 202 " --> pdb=" O SER G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 230 Processing helix chain 'G' and resid 231 through 242 Processing helix chain 'G' and resid 255 through 266 Processing helix chain 'G' and resid 280 through 295 removed outlier: 3.937A pdb=" N LYS G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 304 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 336 through 354 Processing helix chain 'G' and resid 356 through 372 Processing helix chain 'G' and resid 383 through 407 Processing helix chain 'G' and resid 414 through 420 Processing helix chain 'G' and resid 420 through 426 Processing helix chain 'G' and resid 430 through 444 Processing helix chain 'G' and resid 445 through 455 Processing helix chain 'G' and resid 458 through 467 Processing helix chain 'G' and resid 484 through 489 Processing helix chain 'G' and resid 494 through 513 Processing helix chain 'M' and resid 8 through 27 removed outlier: 3.647A pdb=" N ARG M 12 " --> pdb=" O ALA M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 51 through 59 Processing helix chain 'M' and resid 63 through 82 removed outlier: 3.565A pdb=" N LYS M 79 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR M 80 " --> pdb=" O VAL M 76 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP M 82 " --> pdb=" O SER M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 108 removed outlier: 3.820A pdb=" N THR M 90 " --> pdb=" O ASP M 86 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA M 91 " --> pdb=" O GLY M 87 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR M 92 " --> pdb=" O THR M 88 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA M 108 " --> pdb=" O LYS M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 133 Processing helix chain 'M' and resid 139 through 148 Processing helix chain 'M' and resid 154 through 168 removed outlier: 4.001A pdb=" N HIS M 158 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 203 removed outlier: 3.978A pdb=" N MET M 202 " --> pdb=" O SER M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 231 through 242 Processing helix chain 'M' and resid 255 through 266 Processing helix chain 'M' and resid 280 through 295 removed outlier: 3.938A pdb=" N LYS M 284 " --> pdb=" O GLY M 280 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA M 285 " --> pdb=" O ASP M 281 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET M 286 " --> pdb=" O ARG M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 304 Processing helix chain 'M' and resid 306 through 310 Processing helix chain 'M' and resid 336 through 354 Processing helix chain 'M' and resid 356 through 372 Processing helix chain 'M' and resid 383 through 407 Processing helix chain 'M' and resid 414 through 420 Processing helix chain 'M' and resid 420 through 426 Processing helix chain 'M' and resid 431 through 444 Processing helix chain 'M' and resid 445 through 455 Processing helix chain 'M' and resid 458 through 467 Processing helix chain 'M' and resid 484 through 489 Processing helix chain 'M' and resid 494 through 513 Processing helix chain 'H' and resid 8 through 27 removed outlier: 3.722A pdb=" N ARG H 12 " --> pdb=" O ALA H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 51 through 59 Processing helix chain 'H' and resid 63 through 82 removed outlier: 3.957A pdb=" N LYS H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 108 removed outlier: 3.827A pdb=" N THR H 90 " --> pdb=" O ASP H 86 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR H 92 " --> pdb=" O THR H 88 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA H 108 " --> pdb=" O LYS H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 133 Processing helix chain 'H' and resid 139 through 148 Processing helix chain 'H' and resid 154 through 168 removed outlier: 4.046A pdb=" N HIS H 158 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 removed outlier: 3.921A pdb=" N MET H 202 " --> pdb=" O SER H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 230 Processing helix chain 'H' and resid 231 through 242 Processing helix chain 'H' and resid 255 through 266 Processing helix chain 'H' and resid 280 through 295 removed outlier: 4.026A pdb=" N LYS H 284 " --> pdb=" O GLY H 280 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 285 " --> pdb=" O ASP H 281 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET H 286 " --> pdb=" O ARG H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 336 through 354 Processing helix chain 'H' and resid 356 through 373 removed outlier: 4.206A pdb=" N GLY H 373 " --> pdb=" O LYS H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 407 Processing helix chain 'H' and resid 414 through 420 Processing helix chain 'H' and resid 420 through 426 Processing helix chain 'H' and resid 430 through 444 Processing helix chain 'H' and resid 445 through 455 Processing helix chain 'H' and resid 458 through 467 Processing helix chain 'H' and resid 484 through 489 Processing helix chain 'H' and resid 494 through 513 Processing helix chain 'N' and resid 8 through 27 removed outlier: 3.734A pdb=" N ARG N 12 " --> pdb=" O ALA N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 30 No H-bonds generated for 'chain 'N' and resid 28 through 30' Processing helix chain 'N' and resid 51 through 59 removed outlier: 3.501A pdb=" N ILE N 55 " --> pdb=" O ASP N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 82 removed outlier: 3.550A pdb=" N LYS N 79 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP N 82 " --> pdb=" O SER N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 108 removed outlier: 3.829A pdb=" N THR N 90 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA N 91 " --> pdb=" O GLY N 87 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR N 92 " --> pdb=" O THR N 88 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA N 108 " --> pdb=" O LYS N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 133 Processing helix chain 'N' and resid 139 through 148 Processing helix chain 'N' and resid 154 through 168 removed outlier: 4.052A pdb=" N HIS N 158 " --> pdb=" O ASP N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 203 removed outlier: 3.970A pdb=" N MET N 202 " --> pdb=" O SER N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 230 Processing helix chain 'N' and resid 231 through 242 Processing helix chain 'N' and resid 255 through 266 Processing helix chain 'N' and resid 280 through 295 removed outlier: 4.054A pdb=" N LYS N 284 " --> pdb=" O GLY N 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA N 285 " --> pdb=" O ASP N 281 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET N 286 " --> pdb=" O ARG N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 304 Processing helix chain 'N' and resid 336 through 354 Processing helix chain 'N' and resid 356 through 372 Processing helix chain 'N' and resid 383 through 407 Processing helix chain 'N' and resid 414 through 420 Processing helix chain 'N' and resid 420 through 426 Processing helix chain 'N' and resid 430 through 444 Processing helix chain 'N' and resid 445 through 455 Processing helix chain 'N' and resid 458 through 467 Processing helix chain 'N' and resid 484 through 489 Processing helix chain 'N' and resid 494 through 513 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 3.533A pdb=" N VAL D 38 " --> pdb=" O ALA A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.281A pdb=" N VAL A 38 " --> pdb=" O VAL C 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.541A pdb=" N GLY A 333 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA A 318 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 214 removed outlier: 8.517A pdb=" N ILE A 299 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 220 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA7, first strand: chain 'A' and resid 409 through 411 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 476 removed outlier: 3.543A pdb=" N VAL A 483 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 481 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.447A pdb=" N VAL B 38 " --> pdb=" O VAL J 518 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.492A pdb=" N GLY B 333 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA B 318 " --> pdb=" O GLY B 333 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 211 through 214 removed outlier: 8.522A pdb=" N ILE B 299 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE B 220 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB6, first strand: chain 'B' and resid 409 through 411 Processing sheet with id=AB7, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB8, first strand: chain 'C' and resid 172 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 190 through 193 removed outlier: 6.518A pdb=" N GLY C 333 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA C 318 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 211 through 214 removed outlier: 8.522A pdb=" N ILE C 299 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE C 220 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'C' and resid 409 through 411 Processing sheet with id=AC4, first strand: chain 'C' and resid 473 through 476 removed outlier: 3.565A pdb=" N VAL C 483 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 481 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 6 through 7 removed outlier: 3.579A pdb=" N VAL N 38 " --> pdb=" O ALA I 516 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU N 47 " --> pdb=" O LEU N 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 172 through 177 Processing sheet with id=AC7, first strand: chain 'I' and resid 190 through 193 removed outlier: 6.532A pdb=" N GLY I 333 " --> pdb=" O ALA I 318 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA I 318 " --> pdb=" O GLY I 333 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR I 217 " --> pdb=" O LEU I 246 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE I 248 " --> pdb=" O TYR I 217 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU I 219 " --> pdb=" O ILE I 248 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 211 through 214 removed outlier: 8.577A pdb=" N ILE I 299 " --> pdb=" O ILE I 218 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE I 220 " --> pdb=" O ILE I 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 224 through 225 Processing sheet with id=AD1, first strand: chain 'I' and resid 409 through 411 Processing sheet with id=AD2, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 172 through 177 Processing sheet with id=AD4, first strand: chain 'D' and resid 190 through 193 removed outlier: 6.542A pdb=" N GLY D 333 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA D 318 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 245 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL D 274 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE D 247 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 211 through 214 removed outlier: 8.529A pdb=" N ILE D 299 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE D 220 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AD7, first strand: chain 'D' and resid 409 through 411 Processing sheet with id=AD8, first strand: chain 'J' and resid 37 through 38 Processing sheet with id=AD9, first strand: chain 'J' and resid 172 through 177 Processing sheet with id=AE1, first strand: chain 'J' and resid 190 through 193 removed outlier: 6.504A pdb=" N GLY J 333 " --> pdb=" O ALA J 318 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA J 318 " --> pdb=" O GLY J 333 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 211 through 214 removed outlier: 8.511A pdb=" N ILE J 299 " --> pdb=" O ILE J 218 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE J 220 " --> pdb=" O ILE J 299 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 224 through 225 Processing sheet with id=AE4, first strand: chain 'J' and resid 409 through 411 Processing sheet with id=AE5, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AE6, first strand: chain 'E' and resid 37 through 39 Processing sheet with id=AE7, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AE8, first strand: chain 'E' and resid 190 through 193 removed outlier: 6.550A pdb=" N GLY E 333 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA E 318 " --> pdb=" O GLY E 333 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 211 through 214 removed outlier: 8.516A pdb=" N ILE E 299 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE E 220 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 224 through 225 Processing sheet with id=AF2, first strand: chain 'E' and resid 409 through 411 Processing sheet with id=AF3, first strand: chain 'K' and resid 6 through 7 Processing sheet with id=AF4, first strand: chain 'K' and resid 37 through 39 Processing sheet with id=AF5, first strand: chain 'K' and resid 172 through 177 Processing sheet with id=AF6, first strand: chain 'K' and resid 190 through 193 removed outlier: 6.504A pdb=" N GLY K 333 " --> pdb=" O ALA K 318 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA K 318 " --> pdb=" O GLY K 333 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR K 217 " --> pdb=" O LEU K 246 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE K 248 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU K 219 " --> pdb=" O ILE K 248 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 211 through 214 removed outlier: 8.520A pdb=" N ILE K 299 " --> pdb=" O ILE K 218 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE K 220 " --> pdb=" O ILE K 299 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 224 through 225 Processing sheet with id=AF9, first strand: chain 'K' and resid 409 through 411 Processing sheet with id=AG1, first strand: chain 'F' and resid 6 through 7 removed outlier: 6.720A pdb=" N ALA F 516 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 37 through 39 Processing sheet with id=AG3, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AG4, first strand: chain 'F' and resid 190 through 193 removed outlier: 6.520A pdb=" N GLY F 333 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA F 318 " --> pdb=" O GLY F 333 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR F 217 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE F 248 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU F 219 " --> pdb=" O ILE F 248 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 211 through 214 removed outlier: 8.593A pdb=" N ILE F 299 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE F 220 " --> pdb=" O ILE F 299 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 224 through 225 Processing sheet with id=AG7, first strand: chain 'F' and resid 409 through 411 Processing sheet with id=AG8, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AG9, first strand: chain 'L' and resid 47 through 49 removed outlier: 6.344A pdb=" N VAL L 38 " --> pdb=" O VAL M 518 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 172 through 177 Processing sheet with id=AH2, first strand: chain 'L' and resid 190 through 193 removed outlier: 6.545A pdb=" N GLY L 333 " --> pdb=" O ALA L 318 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA L 318 " --> pdb=" O GLY L 333 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU L 245 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL L 274 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE L 247 " --> pdb=" O VAL L 274 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 211 through 214 removed outlier: 8.525A pdb=" N ILE L 299 " --> pdb=" O ILE L 218 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE L 220 " --> pdb=" O ILE L 299 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 224 through 225 Processing sheet with id=AH5, first strand: chain 'L' and resid 409 through 411 Processing sheet with id=AH6, first strand: chain 'G' and resid 6 through 7 removed outlier: 3.594A pdb=" N VAL H 38 " --> pdb=" O ALA G 516 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 172 through 177 Processing sheet with id=AH8, first strand: chain 'G' and resid 190 through 193 removed outlier: 6.518A pdb=" N GLY G 333 " --> pdb=" O ALA G 318 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA G 318 " --> pdb=" O GLY G 333 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR G 217 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU G 245 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL G 274 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE G 247 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 211 through 214 removed outlier: 8.572A pdb=" N ILE G 299 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE G 220 " --> pdb=" O ILE G 299 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AI2, first strand: chain 'G' and resid 409 through 411 Processing sheet with id=AI3, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AI4, first strand: chain 'M' and resid 172 through 177 Processing sheet with id=AI5, first strand: chain 'M' and resid 190 through 193 removed outlier: 6.557A pdb=" N GLY M 333 " --> pdb=" O ALA M 318 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA M 318 " --> pdb=" O GLY M 333 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 211 through 214 removed outlier: 8.546A pdb=" N ILE M 299 " --> pdb=" O ILE M 218 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE M 220 " --> pdb=" O ILE M 299 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 224 through 225 Processing sheet with id=AI8, first strand: chain 'M' and resid 409 through 411 Processing sheet with id=AI9, first strand: chain 'H' and resid 172 through 177 Processing sheet with id=AJ1, first strand: chain 'H' and resid 190 through 193 removed outlier: 6.502A pdb=" N GLY H 333 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA H 318 " --> pdb=" O GLY H 333 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 211 through 214 removed outlier: 8.532A pdb=" N ILE H 299 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE H 220 " --> pdb=" O ILE H 299 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'H' and resid 224 through 225 Processing sheet with id=AJ4, first strand: chain 'H' and resid 409 through 411 Processing sheet with id=AJ5, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AJ6, first strand: chain 'N' and resid 172 through 177 Processing sheet with id=AJ7, first strand: chain 'N' and resid 190 through 193 removed outlier: 6.529A pdb=" N GLY N 333 " --> pdb=" O ALA N 318 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA N 318 " --> pdb=" O GLY N 333 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR N 217 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE N 248 " --> pdb=" O TYR N 217 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU N 219 " --> pdb=" O ILE N 248 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 211 through 214 removed outlier: 8.586A pdb=" N ILE N 299 " --> pdb=" O ILE N 218 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE N 220 " --> pdb=" O ILE N 299 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'N' and resid 224 through 225 Processing sheet with id=AK1, first strand: chain 'N' and resid 409 through 411 3531 hydrogen bonds defined for protein. 9999 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: 26.18 Time building geometry restraints manager: 13.31 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: 18801 1.34 - 1.46: 5847 1.46 - 1.58: 29994 1.58 - 1.70: 0 1.70 - 1.82: 280 Bond restraints: 54922 Sorted by residual: bond pdb=" C ASN M 215 " pdb=" O ASN M 215 " ideal model delta sigma weight residual 1.235 1.217 0.018 4.70e-03 4.53e+04 1.44e+01 bond pdb=" C ASN A 215 " pdb=" O ASN A 215 " ideal model delta sigma weight residual 1.235 1.243 -0.008 4.70e-03 4.53e+04 2.80e+00 bond pdb=" C ASN K 215 " pdb=" O ASN K 215 " ideal model delta sigma weight residual 1.235 1.242 -0.007 4.70e-03 4.53e+04 2.50e+00 bond pdb=" C ASN C 215 " pdb=" O ASN C 215 " ideal model delta sigma weight residual 1.235 1.242 -0.007 4.70e-03 4.53e+04 2.46e+00 bond pdb=" C ASN F 215 " pdb=" O ASN F 215 " ideal model delta sigma weight residual 1.235 1.242 -0.007 4.70e-03 4.53e+04 2.42e+00 ... (remaining 54917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 73713 2.29 - 4.59: 469 4.59 - 6.88: 157 6.88 - 9.17: 19 9.17 - 11.47: 10 Bond angle restraints: 74368 Sorted by residual: angle pdb=" C ALA K 8 " pdb=" CA ALA K 8 " pdb=" CB ALA K 8 " ideal model delta sigma weight residual 116.63 109.88 6.75 1.16e+00 7.43e-01 3.38e+01 angle pdb=" C ALA D 84 " pdb=" CA ALA D 84 " pdb=" CB ALA D 84 " ideal model delta sigma weight residual 115.79 110.14 5.65 1.19e+00 7.06e-01 2.26e+01 angle pdb=" C ALA L 84 " pdb=" CA ALA L 84 " pdb=" CB ALA L 84 " ideal model delta sigma weight residual 115.79 110.15 5.64 1.19e+00 7.06e-01 2.25e+01 angle pdb=" C ALA M 84 " pdb=" CA ALA M 84 " pdb=" CB ALA M 84 " ideal model delta sigma weight residual 115.79 110.16 5.63 1.19e+00 7.06e-01 2.24e+01 angle pdb=" C ALA N 84 " pdb=" CA ALA N 84 " pdb=" CB ALA N 84 " ideal model delta sigma weight residual 115.79 110.18 5.61 1.19e+00 7.06e-01 2.22e+01 ... (remaining 74363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 30899 17.17 - 34.35: 2480 34.35 - 51.52: 409 51.52 - 68.70: 164 68.70 - 85.87: 26 Dihedral angle restraints: 33978 sinusoidal: 13146 harmonic: 20832 Sorted by residual: dihedral pdb=" CA SER A 150 " pdb=" C SER A 150 " pdb=" N SER A 151 " pdb=" CA SER A 151 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA VAL D 149 " pdb=" C VAL D 149 " pdb=" N SER D 150 " pdb=" CA SER D 150 " ideal model delta harmonic sigma weight residual 180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA SER E 153 " pdb=" C SER E 153 " pdb=" N ASP E 154 " pdb=" CA ASP E 154 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 33975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 6786 0.036 - 0.073: 1734 0.073 - 0.109: 599 0.109 - 0.145: 155 0.145 - 0.181: 8 Chirality restraints: 9282 Sorted by residual: chirality pdb=" CA MET H 286 " pdb=" N MET H 286 " pdb=" C MET H 286 " pdb=" CB MET H 286 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA MET K 286 " pdb=" N MET K 286 " pdb=" C MET K 286 " pdb=" CB MET K 286 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA MET M 286 " pdb=" N MET M 286 " pdb=" C MET M 286 " pdb=" CB MET M 286 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 9279 not shown) Planarity restraints: 9674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 209 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C MET I 209 " -0.033 2.00e-02 2.50e+03 pdb=" O MET I 209 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU I 210 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET K 209 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C MET K 209 " 0.032 2.00e-02 2.50e+03 pdb=" O MET K 209 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU K 210 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 209 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C MET F 209 " -0.032 2.00e-02 2.50e+03 pdb=" O MET F 209 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU F 210 " 0.011 2.00e-02 2.50e+03 ... (remaining 9671 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 8538 2.76 - 3.29: 56383 3.29 - 3.83: 95070 3.83 - 4.36: 106057 4.36 - 4.90: 183453 Nonbonded interactions: 449501 Sorted by model distance: nonbonded pdb=" OG1 THR E 135 " pdb=" O MET E 409 " model vdw 2.222 3.040 nonbonded pdb=" OG SER E 153 " pdb=" N ASP E 154 " model vdw 2.232 3.120 nonbonded pdb=" O ALA C 397 " pdb=" OG1 THR C 401 " model vdw 2.239 3.040 nonbonded pdb=" O ALA K 397 " pdb=" OG1 THR K 401 " model vdw 2.246 3.040 nonbonded pdb=" O ALA L 397 " pdb=" OG1 THR L 401 " model vdw 2.247 3.040 ... (remaining 449496 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = 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' } 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: 0.750 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: 0.070 Extract box with map and model: 1.750 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 103.320 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.003 0.047 54922 Z= 0.191 Angle : 0.561 11.467 74368 Z= 0.312 Chirality : 0.039 0.181 9282 Planarity : 0.002 0.026 9674 Dihedral : 13.214 85.872 20538 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 0.08 % Allowed : 10.30 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.10), residues: 7308 helix: 2.16 (0.08), residues: 3906 sheet: 0.28 (0.17), residues: 1022 loop : -0.10 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.006 0.001 HIS K 64 PHE 0.013 0.001 PHE F 7 TYR 0.006 0.001 TYR I 197 ARG 0.006 0.000 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 279 time to evaluate : 5.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3709 (ptp) cc_final: 0.3336 (mpp) REVERT: C 15 MET cc_start: 0.8185 (mmm) cc_final: 0.7699 (mmt) REVERT: C 485 MET cc_start: 0.7080 (mmm) cc_final: 0.6775 (mmt) REVERT: I 191 MET cc_start: 0.8502 (mmm) cc_final: 0.8028 (mmm) REVERT: D 1 MET cc_start: 0.4078 (ptt) cc_final: 0.3264 (mpp) REVERT: J 15 MET cc_start: 0.7519 (mmm) cc_final: 0.7059 (mmm) REVERT: J 47 LEU cc_start: 0.8207 (tp) cc_final: 0.7836 (mm) REVERT: J 209 MET cc_start: 0.8047 (tmm) cc_final: 0.7798 (tmm) REVERT: K 68 MET cc_start: 0.7519 (mmm) cc_final: 0.7059 (mmt) REVERT: K 260 LEU cc_start: 0.8443 (mt) cc_final: 0.8074 (pp) REVERT: F 202 MET cc_start: -0.0275 (ptt) cc_final: -0.0500 (ptp) REVERT: L 1 MET cc_start: 0.3988 (ptt) cc_final: 0.3642 (mpp) REVERT: L 15 MET cc_start: 0.7940 (mmm) cc_final: 0.7694 (mmm) REVERT: L 68 MET cc_start: 0.7249 (mmm) cc_final: 0.6988 (mmm) REVERT: L 164 MET cc_start: 0.7619 (tpt) cc_final: 0.7365 (mmm) REVERT: G 15 MET cc_start: 0.7979 (mmm) cc_final: 0.7651 (mmt) REVERT: G 209 MET cc_start: 0.7495 (tmm) cc_final: 0.7262 (tmm) REVERT: M 209 MET cc_start: 0.7564 (tmm) cc_final: 0.7345 (tmm) REVERT: H 1 MET cc_start: 0.4390 (ptt) cc_final: 0.3669 (mpp) REVERT: N 191 MET cc_start: 0.8299 (mmm) cc_final: 0.7872 (mmm) REVERT: N 286 MET cc_start: 0.7748 (pmm) cc_final: 0.7417 (ptp) outliers start: 5 outliers final: 3 residues processed: 283 average time/residue: 0.4677 time to fit residues: 236.1164 Evaluate side-chains 171 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain G residue 138 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 0.0170 chunk 551 optimal weight: 50.0000 chunk 306 optimal weight: 8.9990 chunk 188 optimal weight: 40.0000 chunk 372 optimal weight: 9.9990 chunk 294 optimal weight: 8.9990 chunk 570 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 346 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 chunk 661 optimal weight: 8.9990 overall best weight: 3.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 ASN B 81 ASN B 96 GLN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 105 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN J 81 ASN J 96 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 ASN K 81 ASN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 503 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN L 81 ASN ** L 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 503 ASN M 81 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 503 ASN ** H 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 503 ASN N 81 ASN N 105 ASN ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 503 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.118346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093854 restraints weight = 200918.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092787 restraints weight = 170382.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093347 restraints weight = 135258.883| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54922 Z= 0.225 Angle : 0.533 7.287 74368 Z= 0.291 Chirality : 0.043 0.187 9282 Planarity : 0.003 0.033 9674 Dihedral : 3.890 25.204 7664 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 0.98 % Allowed : 10.59 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.10), residues: 7308 helix: 2.08 (0.08), residues: 4032 sheet: 0.04 (0.20), residues: 728 loop : -0.05 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 482 HIS 0.004 0.001 HIS B 64 PHE 0.008 0.001 PHE G 7 TYR 0.006 0.001 TYR N 43 ARG 0.004 0.001 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5202 (ptp) cc_final: 0.4384 (mpp) REVERT: A 68 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7898 (mmm) REVERT: A 209 MET cc_start: 0.7839 (tmm) cc_final: 0.7614 (tmm) REVERT: A 286 MET cc_start: 0.7380 (pmm) cc_final: 0.7141 (pmm) REVERT: B 7 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: C 15 MET cc_start: 0.8748 (mmm) cc_final: 0.8104 (tpp) REVERT: C 485 MET cc_start: 0.7827 (mmm) cc_final: 0.7005 (mmt) REVERT: I 286 MET cc_start: 0.6974 (pmm) cc_final: 0.6626 (pmm) REVERT: D 1 MET cc_start: 0.5475 (ptt) cc_final: 0.4395 (mpp) REVERT: D 68 MET cc_start: 0.8353 (mmm) cc_final: 0.7991 (mtp) REVERT: D 96 GLN cc_start: 0.8018 (tt0) cc_final: 0.7811 (tt0) REVERT: J 15 MET cc_start: 0.8467 (mmm) cc_final: 0.7871 (mmm) REVERT: J 209 MET cc_start: 0.8073 (tmm) cc_final: 0.7823 (tmm) REVERT: E 1 MET cc_start: 0.4662 (OUTLIER) cc_final: 0.3768 (mpp) REVERT: E 164 MET cc_start: 0.7627 (mmm) cc_final: 0.7248 (mmm) REVERT: K 15 MET cc_start: 0.8600 (mmm) cc_final: 0.8079 (mmt) REVERT: K 75 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6071 (tm-30) REVERT: K 164 MET cc_start: 0.8551 (mmm) cc_final: 0.8239 (mmm) REVERT: K 260 LEU cc_start: 0.7953 (mt) cc_final: 0.7715 (pp) REVERT: K 286 MET cc_start: 0.7822 (pmm) cc_final: 0.7461 (pmm) REVERT: F 164 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7422 (ttp) REVERT: F 209 MET cc_start: 0.7858 (tmm) cc_final: 0.7611 (tmm) REVERT: L 1 MET cc_start: 0.5072 (ptt) cc_final: 0.4634 (mpp) REVERT: L 15 MET cc_start: 0.8642 (mmm) cc_final: 0.8338 (mmm) REVERT: L 209 MET cc_start: 0.7798 (tmm) cc_final: 0.7586 (tmm) REVERT: G 15 MET cc_start: 0.8733 (mmm) cc_final: 0.8362 (mmt) REVERT: G 209 MET cc_start: 0.7717 (tmm) cc_final: 0.7371 (tmm) REVERT: G 286 MET cc_start: 0.7458 (pmm) cc_final: 0.7122 (pmm) REVERT: M 286 MET cc_start: 0.7738 (pmm) cc_final: 0.7269 (ptp) REVERT: M 485 MET cc_start: 0.8517 (mmm) cc_final: 0.8153 (mmt) REVERT: H 1 MET cc_start: 0.5826 (ptt) cc_final: 0.5189 (mpp) REVERT: H 164 MET cc_start: 0.8354 (ttp) cc_final: 0.7701 (mtp) REVERT: N 286 MET cc_start: 0.7432 (pmm) cc_final: 0.7150 (ptp) REVERT: N 511 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8310 (tt) outliers start: 58 outliers final: 20 residues processed: 225 average time/residue: 0.4791 time to fit residues: 194.3165 Evaluate side-chains 188 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 511 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 115 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 439 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 376 optimal weight: 7.9990 chunk 435 optimal weight: 10.0000 chunk 615 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 241 GLN C 105 ASN C 241 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN J 96 GLN J 105 ASN J 241 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 ASN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN L 241 GLN G 241 GLN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN ** M 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN ** H 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.092563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.068194 restraints weight = 207263.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.067932 restraints weight = 195473.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.068243 restraints weight = 138595.011| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54922 Z= 0.280 Angle : 0.552 10.845 74368 Z= 0.299 Chirality : 0.042 0.146 9282 Planarity : 0.003 0.031 9674 Dihedral : 3.996 30.661 7662 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.57 % Favored : 96.29 % Rotamer: Outliers : 1.43 % Allowed : 11.18 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.10), residues: 7308 helix: 2.01 (0.08), residues: 3990 sheet: -0.21 (0.18), residues: 896 loop : -0.17 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.006 0.001 HIS A 64 PHE 0.021 0.002 PHE D 7 TYR 0.005 0.001 TYR H 43 ARG 0.005 0.001 ARG J 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 166 time to evaluate : 4.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5519 (ptp) cc_final: 0.4827 (mpp) REVERT: A 202 MET cc_start: 0.2655 (ptp) cc_final: 0.2154 (ptt) REVERT: B 15 MET cc_start: 0.8780 (mmm) cc_final: 0.8511 (tpp) REVERT: C 15 MET cc_start: 0.8848 (mmm) cc_final: 0.8395 (tpp) REVERT: C 164 MET cc_start: 0.7743 (mmm) cc_final: 0.7436 (mmm) REVERT: C 485 MET cc_start: 0.8294 (mmm) cc_final: 0.7884 (mmt) REVERT: I 164 MET cc_start: 0.7871 (ttm) cc_final: 0.7418 (mtp) REVERT: I 209 MET cc_start: 0.7144 (tmm) cc_final: 0.6929 (tmm) REVERT: D 1 MET cc_start: 0.5875 (ptt) cc_final: 0.5140 (mpp) REVERT: D 209 MET cc_start: 0.7452 (tmm) cc_final: 0.7206 (tmm) REVERT: J 286 MET cc_start: 0.7564 (pmm) cc_final: 0.7300 (pmm) REVERT: E 1 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.4107 (mpp) REVERT: E 164 MET cc_start: 0.7469 (mmm) cc_final: 0.7039 (mmm) REVERT: K 15 MET cc_start: 0.8716 (mmm) cc_final: 0.8121 (mmt) REVERT: K 75 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6150 (tm-30) REVERT: K 96 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: K 164 MET cc_start: 0.8465 (mmm) cc_final: 0.8192 (mmm) REVERT: F 1 MET cc_start: 0.6615 (mpp) cc_final: 0.6312 (mpp) REVERT: L 1 MET cc_start: 0.5164 (ptt) cc_final: 0.4845 (mpp) REVERT: L 15 MET cc_start: 0.8621 (mmm) cc_final: 0.8345 (mmm) REVERT: L 164 MET cc_start: 0.7605 (mmm) cc_final: 0.7380 (mmm) REVERT: G 10 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.6232 (p0) REVERT: G 15 MET cc_start: 0.8739 (mmm) cc_final: 0.8424 (tpp) REVERT: G 96 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: G 164 MET cc_start: 0.7800 (tpt) cc_final: 0.7194 (mmm) REVERT: G 209 MET cc_start: 0.7393 (tmm) cc_final: 0.7145 (tmm) REVERT: M 511 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8495 (tt) REVERT: H 1 MET cc_start: 0.5702 (ptp) cc_final: 0.5398 (mpp) REVERT: H 15 MET cc_start: 0.8491 (tpp) cc_final: 0.8147 (tpp) REVERT: H 202 MET cc_start: 0.1683 (ptp) cc_final: 0.1149 (ptp) REVERT: H 511 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8600 (tt) REVERT: N 511 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8354 (tt) outliers start: 84 outliers final: 46 residues processed: 243 average time/residue: 0.4608 time to fit residues: 201.5804 Evaluate side-chains 211 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 4.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 202 MET Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 511 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 511 LEU Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 511 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 264 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 438 optimal weight: 0.0970 chunk 239 optimal weight: 30.0000 chunk 408 optimal weight: 6.9990 chunk 223 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 595 optimal weight: 8.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN K 241 GLN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN N 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.111857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087357 restraints weight = 203353.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085583 restraints weight = 193307.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085878 restraints weight = 152787.568| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 54922 Z= 0.243 Angle : 0.511 12.003 74368 Z= 0.276 Chirality : 0.041 0.143 9282 Planarity : 0.003 0.036 9674 Dihedral : 3.978 27.417 7662 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.41 % Rotamer: Outliers : 1.43 % Allowed : 11.76 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 7308 helix: 1.95 (0.08), residues: 4032 sheet: -0.20 (0.18), residues: 896 loop : -0.17 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 482 HIS 0.004 0.001 HIS L 64 PHE 0.021 0.001 PHE B 7 TYR 0.005 0.001 TYR B 197 ARG 0.007 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 162 time to evaluate : 5.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5641 (ptp) cc_final: 0.4960 (mpp) REVERT: C 15 MET cc_start: 0.8799 (mmm) cc_final: 0.8345 (tpp) REVERT: C 164 MET cc_start: 0.7991 (mmm) cc_final: 0.7659 (mmm) REVERT: C 209 MET cc_start: 0.7856 (tmm) cc_final: 0.7609 (tmm) REVERT: C 485 MET cc_start: 0.8329 (mmm) cc_final: 0.7840 (mmt) REVERT: I 164 MET cc_start: 0.8308 (ttm) cc_final: 0.7988 (mtp) REVERT: I 209 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7270 (tmm) REVERT: D 1 MET cc_start: 0.5938 (ptt) cc_final: 0.5205 (mpp) REVERT: D 221 THR cc_start: 0.6329 (OUTLIER) cc_final: 0.6013 (t) REVERT: J 164 MET cc_start: 0.7779 (mmm) cc_final: 0.7569 (mmm) REVERT: E 1 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.4415 (mpp) REVERT: E 164 MET cc_start: 0.7955 (mmm) cc_final: 0.7360 (mmm) REVERT: E 511 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8236 (tt) REVERT: K 15 MET cc_start: 0.8739 (mmm) cc_final: 0.8190 (mmt) REVERT: K 75 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: K 164 MET cc_start: 0.8939 (mmm) cc_final: 0.8490 (mmm) REVERT: F 1 MET cc_start: 0.6750 (mpp) cc_final: 0.6491 (mpp) REVERT: F 164 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7379 (mtp) REVERT: L 1 MET cc_start: 0.5329 (ptt) cc_final: 0.4793 (mpp) REVERT: L 15 MET cc_start: 0.8549 (mmm) cc_final: 0.8273 (mmm) REVERT: L 221 THR cc_start: 0.5508 (OUTLIER) cc_final: 0.5190 (t) REVERT: G 164 MET cc_start: 0.8118 (tpt) cc_final: 0.7570 (mmm) REVERT: G 209 MET cc_start: 0.7795 (tmm) cc_final: 0.7468 (tmm) REVERT: M 485 MET cc_start: 0.8622 (mmm) cc_final: 0.7784 (mmm) REVERT: H 1 MET cc_start: 0.5960 (ptp) cc_final: 0.5534 (mpp) REVERT: H 164 MET cc_start: 0.8305 (mtp) cc_final: 0.7910 (mmm) REVERT: H 202 MET cc_start: 0.2409 (ptp) cc_final: 0.2101 (ptt) REVERT: N 209 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7066 (tmm) REVERT: N 511 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8271 (tt) outliers start: 84 outliers final: 39 residues processed: 237 average time/residue: 0.4606 time to fit residues: 197.8828 Evaluate side-chains 205 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 507 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 209 MET Chi-restraints excluded: chain N residue 433 VAL Chi-restraints excluded: chain N residue 511 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 599 optimal weight: 8.9990 chunk 456 optimal weight: 0.7980 chunk 386 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 660 optimal weight: 30.0000 chunk 497 optimal weight: 20.0000 chunk 426 optimal weight: 0.9990 chunk 409 optimal weight: 5.9990 chunk 557 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 534 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN F 105 ASN F 241 GLN G 96 GLN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097719 restraints weight = 198841.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095116 restraints weight = 174320.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095482 restraints weight = 141427.684| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54922 Z= 0.204 Angle : 0.494 9.957 74368 Z= 0.265 Chirality : 0.041 0.157 9282 Planarity : 0.003 0.029 9674 Dihedral : 3.914 25.381 7662 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 1.78 % Allowed : 12.42 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 7308 helix: 2.04 (0.08), residues: 4032 sheet: -0.00 (0.17), residues: 1008 loop : -0.44 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 482 HIS 0.003 0.001 HIS E 64 PHE 0.017 0.001 PHE B 7 TYR 0.006 0.001 TYR I 197 ARG 0.008 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 167 time to evaluate : 5.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5594 (ptp) cc_final: 0.4939 (mpp) REVERT: A 164 MET cc_start: 0.7441 (mmm) cc_final: 0.7114 (mmm) REVERT: A 286 MET cc_start: 0.7764 (pmm) cc_final: 0.7545 (pmm) REVERT: B 164 MET cc_start: 0.8754 (mtp) cc_final: 0.8402 (mmm) REVERT: C 15 MET cc_start: 0.8821 (mmm) cc_final: 0.8357 (tpp) REVERT: C 103 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8853 (mp) REVERT: C 164 MET cc_start: 0.8302 (mmm) cc_final: 0.8079 (mmm) REVERT: C 209 MET cc_start: 0.8019 (tmm) cc_final: 0.7685 (tmm) REVERT: C 286 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7788 (pmm) REVERT: I 38 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8978 (m) REVERT: I 164 MET cc_start: 0.8511 (ttm) cc_final: 0.8284 (mtp) REVERT: I 209 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7352 (tmm) REVERT: I 286 MET cc_start: 0.7415 (pmm) cc_final: 0.7144 (pmm) REVERT: D 1 MET cc_start: 0.5941 (ptt) cc_final: 0.5214 (mpp) REVERT: D 164 MET cc_start: 0.8293 (ptm) cc_final: 0.7992 (mtp) REVERT: D 209 MET cc_start: 0.7484 (tmm) cc_final: 0.7220 (tmm) REVERT: D 221 THR cc_start: 0.6366 (OUTLIER) cc_final: 0.6095 (t) REVERT: J 164 MET cc_start: 0.7863 (mmm) cc_final: 0.7594 (mmm) REVERT: E 1 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.4859 (mpp) REVERT: E 164 MET cc_start: 0.8039 (mmm) cc_final: 0.7399 (mmm) REVERT: E 511 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8131 (tt) REVERT: K 15 MET cc_start: 0.8803 (mmm) cc_final: 0.8354 (mmt) REVERT: K 164 MET cc_start: 0.9024 (mmm) cc_final: 0.8504 (mmm) REVERT: F 1 MET cc_start: 0.6321 (mpp) cc_final: 0.6092 (mpp) REVERT: F 164 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7720 (mtp) REVERT: L 1 MET cc_start: 0.5396 (ptt) cc_final: 0.5091 (mpp) REVERT: L 164 MET cc_start: 0.7962 (mmm) cc_final: 0.7547 (mmm) REVERT: G 164 MET cc_start: 0.8435 (tpt) cc_final: 0.8019 (mmm) REVERT: G 209 MET cc_start: 0.7841 (tmm) cc_final: 0.7490 (tmm) REVERT: M 286 MET cc_start: 0.7945 (mpp) cc_final: 0.6943 (ptp) REVERT: M 485 MET cc_start: 0.8591 (mmm) cc_final: 0.7771 (mmm) REVERT: H 1 MET cc_start: 0.5788 (ptp) cc_final: 0.5378 (mpp) REVERT: H 164 MET cc_start: 0.8518 (mtp) cc_final: 0.7958 (mmm) REVERT: H 286 MET cc_start: 0.8237 (pmm) cc_final: 0.7879 (pmm) outliers start: 105 outliers final: 55 residues processed: 260 average time/residue: 0.4549 time to fit residues: 214.1210 Evaluate side-chains 221 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 507 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 507 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 507 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 285 optimal weight: 5.9990 chunk 440 optimal weight: 20.0000 chunk 704 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 580 optimal weight: 20.0000 chunk 435 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 418 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 241 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 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 = 0.3982 r_free = 0.3982 target = 0.091781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.067382 restraints weight = 206923.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066340 restraints weight = 223756.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066659 restraints weight = 169954.225| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 54922 Z= 0.254 Angle : 0.532 11.550 74368 Z= 0.284 Chirality : 0.042 0.170 9282 Planarity : 0.003 0.030 9674 Dihedral : 3.969 25.790 7662 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 2.00 % Allowed : 12.74 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.10), residues: 7308 helix: 2.01 (0.08), residues: 4004 sheet: 0.07 (0.16), residues: 1190 loop : -0.33 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.004 0.001 HIS K 64 PHE 0.018 0.001 PHE B 7 TYR 0.007 0.001 TYR J 43 ARG 0.007 0.000 ARG K 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 160 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5718 (ptp) cc_final: 0.5087 (mpp) REVERT: A 164 MET cc_start: 0.7300 (mmm) cc_final: 0.6968 (mmm) REVERT: A 202 MET cc_start: 0.2601 (ptp) cc_final: 0.2194 (ptt) REVERT: C 15 MET cc_start: 0.8765 (mmm) cc_final: 0.8400 (tpp) REVERT: C 103 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8878 (mp) REVERT: C 164 MET cc_start: 0.8241 (mmm) cc_final: 0.8014 (mmm) REVERT: C 209 MET cc_start: 0.7919 (tmm) cc_final: 0.7635 (tmm) REVERT: C 286 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7771 (pmm) REVERT: C 485 MET cc_start: 0.8372 (mmm) cc_final: 0.7778 (mmt) REVERT: I 286 MET cc_start: 0.7184 (pmm) cc_final: 0.6719 (ptp) REVERT: D 1 MET cc_start: 0.5680 (ptt) cc_final: 0.5157 (mpp) REVERT: D 164 MET cc_start: 0.8290 (ptm) cc_final: 0.7990 (mtp) REVERT: D 209 MET cc_start: 0.7539 (tmm) cc_final: 0.7242 (tmm) REVERT: D 221 THR cc_start: 0.6539 (OUTLIER) cc_final: 0.6241 (t) REVERT: D 286 MET cc_start: 0.7952 (pmm) cc_final: 0.7721 (pmm) REVERT: J 164 MET cc_start: 0.7796 (mmm) cc_final: 0.7586 (mmm) REVERT: J 286 MET cc_start: 0.7688 (pmm) cc_final: 0.7483 (pmm) REVERT: E 1 MET cc_start: 0.5646 (OUTLIER) cc_final: 0.4841 (mpp) REVERT: E 164 MET cc_start: 0.8077 (mmm) cc_final: 0.7672 (mmm) REVERT: E 286 MET cc_start: 0.7860 (pmm) cc_final: 0.7607 (pmm) REVERT: E 511 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8354 (tt) REVERT: K 15 MET cc_start: 0.8830 (mmm) cc_final: 0.8356 (tpp) REVERT: K 164 MET cc_start: 0.8813 (mmm) cc_final: 0.8453 (mmm) REVERT: F 1 MET cc_start: 0.6674 (mpp) cc_final: 0.6474 (mpp) REVERT: F 164 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: L 1 MET cc_start: 0.5497 (ptt) cc_final: 0.4988 (mpp) REVERT: L 164 MET cc_start: 0.7565 (mmm) cc_final: 0.7263 (mmm) REVERT: L 221 THR cc_start: 0.5920 (OUTLIER) cc_final: 0.5593 (t) REVERT: L 286 MET cc_start: 0.7885 (pmm) cc_final: 0.7622 (pmm) REVERT: G 164 MET cc_start: 0.8338 (tpt) cc_final: 0.8058 (mmm) REVERT: G 209 MET cc_start: 0.7527 (tmm) cc_final: 0.7306 (tmm) REVERT: M 209 MET cc_start: 0.7540 (tmm) cc_final: 0.7301 (tmm) REVERT: M 286 MET cc_start: 0.7763 (mpp) cc_final: 0.7047 (ptp) REVERT: M 485 MET cc_start: 0.8674 (mmm) cc_final: 0.7860 (mmm) REVERT: H 1 MET cc_start: 0.5736 (ptp) cc_final: 0.5278 (mpp) REVERT: H 164 MET cc_start: 0.8310 (mtp) cc_final: 0.8049 (mmm) REVERT: H 202 MET cc_start: 0.2204 (ptp) cc_final: 0.1933 (ptt) REVERT: N 68 MET cc_start: 0.8548 (mmm) cc_final: 0.8141 (tpp) REVERT: N 103 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8857 (mp) REVERT: N 191 MET cc_start: 0.8128 (mmm) cc_final: 0.7927 (mmm) REVERT: N 511 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8197 (tt) outliers start: 118 outliers final: 71 residues processed: 268 average time/residue: 0.4509 time to fit residues: 219.6359 Evaluate side-chains 239 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 159 time to evaluate : 4.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 507 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 507 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain H residue 507 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 433 VAL Chi-restraints excluded: chain N residue 507 VAL Chi-restraints excluded: chain N residue 511 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 504 optimal weight: 40.0000 chunk 165 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 128 optimal weight: 50.0000 chunk 383 optimal weight: 8.9990 chunk 361 optimal weight: 4.9990 chunk 522 optimal weight: 0.8980 chunk 501 optimal weight: 50.0000 chunk 283 optimal weight: 30.0000 chunk 447 optimal weight: 50.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN E 81 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN L 105 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.091512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067247 restraints weight = 205061.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066143 restraints weight = 220108.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066868 restraints weight = 171467.588| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 54922 Z= 0.232 Angle : 0.517 12.479 74368 Z= 0.274 Chirality : 0.041 0.140 9282 Planarity : 0.003 0.030 9674 Dihedral : 3.957 25.532 7662 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 1.63 % Allowed : 13.49 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.10), residues: 7308 helix: 2.02 (0.08), residues: 4018 sheet: -0.02 (0.15), residues: 1232 loop : -0.50 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 482 HIS 0.004 0.001 HIS B 64 PHE 0.016 0.001 PHE C 7 TYR 0.007 0.001 TYR F 197 ARG 0.006 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 168 time to evaluate : 5.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5902 (ptp) cc_final: 0.5151 (mpp) REVERT: A 164 MET cc_start: 0.7570 (mmm) cc_final: 0.7223 (mmm) REVERT: A 202 MET cc_start: 0.2648 (ptp) cc_final: 0.2336 (ptt) REVERT: A 209 MET cc_start: 0.7517 (tmm) cc_final: 0.7234 (tmm) REVERT: B 164 MET cc_start: 0.8602 (mmm) cc_final: 0.8017 (mmm) REVERT: B 286 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7851 (pmm) REVERT: C 15 MET cc_start: 0.8742 (mmm) cc_final: 0.8381 (tpp) REVERT: C 103 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8824 (mp) REVERT: C 164 MET cc_start: 0.8311 (mmm) cc_final: 0.8103 (mmm) REVERT: C 209 MET cc_start: 0.7900 (tmm) cc_final: 0.7588 (tmm) REVERT: C 286 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7734 (pmm) REVERT: I 164 MET cc_start: 0.8023 (mtp) cc_final: 0.7779 (tmm) REVERT: I 286 MET cc_start: 0.7262 (pmm) cc_final: 0.6936 (ptp) REVERT: D 1 MET cc_start: 0.5714 (ptt) cc_final: 0.5109 (mpp) REVERT: D 105 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8964 (t0) REVERT: D 164 MET cc_start: 0.8335 (ptm) cc_final: 0.8067 (mtp) REVERT: D 209 MET cc_start: 0.7538 (tmm) cc_final: 0.7214 (tmm) REVERT: D 221 THR cc_start: 0.6368 (OUTLIER) cc_final: 0.6080 (t) REVERT: J 1 MET cc_start: 0.6173 (mtp) cc_final: 0.5572 (mpp) REVERT: J 164 MET cc_start: 0.7774 (mmm) cc_final: 0.7536 (mmm) REVERT: E 1 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.4869 (mpp) REVERT: E 164 MET cc_start: 0.8166 (mmm) cc_final: 0.7644 (mmm) REVERT: E 511 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8284 (tt) REVERT: K 15 MET cc_start: 0.8735 (mmm) cc_final: 0.8312 (tpp) REVERT: K 164 MET cc_start: 0.8779 (mmm) cc_final: 0.8322 (mmm) REVERT: K 286 MET cc_start: 0.7717 (pmm) cc_final: 0.7424 (pmm) REVERT: F 1 MET cc_start: 0.6262 (mpp) cc_final: 0.5879 (mpp) REVERT: F 209 MET cc_start: 0.7580 (tmm) cc_final: 0.7287 (tmm) REVERT: L 1 MET cc_start: 0.5460 (ptt) cc_final: 0.4962 (mpp) REVERT: L 164 MET cc_start: 0.7825 (mmm) cc_final: 0.7551 (mmm) REVERT: L 221 THR cc_start: 0.5949 (OUTLIER) cc_final: 0.5620 (t) REVERT: G 164 MET cc_start: 0.8366 (tpt) cc_final: 0.8117 (mmm) REVERT: M 164 MET cc_start: 0.7318 (tpt) cc_final: 0.6880 (mmm) REVERT: M 286 MET cc_start: 0.7737 (mpp) cc_final: 0.7123 (ptt) REVERT: M 485 MET cc_start: 0.8636 (mmm) cc_final: 0.7794 (mmm) REVERT: H 1 MET cc_start: 0.5633 (ptp) cc_final: 0.5203 (mpp) REVERT: H 7 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: H 164 MET cc_start: 0.8251 (mtp) cc_final: 0.8008 (mmm) REVERT: H 202 MET cc_start: 0.2303 (ptp) cc_final: 0.1952 (ptt) REVERT: N 103 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8834 (mp) outliers start: 96 outliers final: 67 residues processed: 255 average time/residue: 0.4666 time to fit residues: 216.9685 Evaluate side-chains 235 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 158 time to evaluate : 5.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 507 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 507 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 507 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 507 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 620 optimal weight: 8.9990 chunk 230 optimal weight: 0.0000 chunk 402 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 chunk 415 optimal weight: 3.9990 chunk 522 optimal weight: 2.9990 chunk 677 optimal weight: 4.9990 chunk 566 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN C 105 ASN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.092511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068217 restraints weight = 205695.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.067569 restraints weight = 203072.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.067859 restraints weight = 154099.738| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 54922 Z= 0.159 Angle : 0.494 13.873 74368 Z= 0.258 Chirality : 0.040 0.146 9282 Planarity : 0.003 0.028 9674 Dihedral : 3.877 25.988 7662 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.27 % Allowed : 13.95 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 7308 helix: 2.12 (0.08), residues: 4018 sheet: -0.06 (0.17), residues: 1050 loop : -0.62 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 482 HIS 0.004 0.001 HIS N 64 PHE 0.015 0.001 PHE C 7 TYR 0.006 0.001 TYR K 197 ARG 0.005 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5812 (ptp) cc_final: 0.5105 (mpp) REVERT: A 164 MET cc_start: 0.7618 (mmm) cc_final: 0.7249 (mmm) REVERT: A 209 MET cc_start: 0.7579 (tmm) cc_final: 0.7261 (tmm) REVERT: A 286 MET cc_start: 0.7490 (pmm) cc_final: 0.7190 (pmm) REVERT: B 15 MET cc_start: 0.8624 (mmm) cc_final: 0.8189 (mmm) REVERT: B 164 MET cc_start: 0.8487 (mmm) cc_final: 0.8024 (mmm) REVERT: B 286 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7897 (pmm) REVERT: C 15 MET cc_start: 0.8676 (mmm) cc_final: 0.8313 (tpp) REVERT: C 103 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8747 (mp) REVERT: C 164 MET cc_start: 0.8368 (mmm) cc_final: 0.8101 (mmm) REVERT: C 209 MET cc_start: 0.7906 (tmm) cc_final: 0.7591 (tmm) REVERT: C 286 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7722 (pmm) REVERT: I 164 MET cc_start: 0.8035 (mtp) cc_final: 0.7786 (mmm) REVERT: I 286 MET cc_start: 0.7217 (pmm) cc_final: 0.6897 (ptp) REVERT: D 1 MET cc_start: 0.5616 (ptt) cc_final: 0.5075 (mpp) REVERT: D 105 ASN cc_start: 0.9320 (OUTLIER) cc_final: 0.9076 (t0) REVERT: D 164 MET cc_start: 0.8367 (ptm) cc_final: 0.8002 (mtp) REVERT: D 209 MET cc_start: 0.7583 (tmm) cc_final: 0.7269 (tmm) REVERT: D 286 MET cc_start: 0.7740 (pmm) cc_final: 0.7504 (pmm) REVERT: J 1 MET cc_start: 0.6191 (mtp) cc_final: 0.5564 (mpp) REVERT: J 164 MET cc_start: 0.7800 (mmm) cc_final: 0.7389 (mmm) REVERT: J 221 THR cc_start: 0.4709 (OUTLIER) cc_final: 0.4449 (t) REVERT: E 1 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.5035 (mpp) REVERT: E 164 MET cc_start: 0.8210 (mmm) cc_final: 0.7668 (mmm) REVERT: E 286 MET cc_start: 0.7674 (pmm) cc_final: 0.7404 (pmm) REVERT: E 511 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8412 (tt) REVERT: K 15 MET cc_start: 0.8587 (mmm) cc_final: 0.8175 (tpp) REVERT: K 164 MET cc_start: 0.8823 (mmm) cc_final: 0.8347 (mmm) REVERT: F 1 MET cc_start: 0.6180 (mpp) cc_final: 0.5817 (mpp) REVERT: F 209 MET cc_start: 0.7676 (tmm) cc_final: 0.7388 (tmm) REVERT: L 1 MET cc_start: 0.5386 (ptt) cc_final: 0.5019 (mpp) REVERT: L 68 MET cc_start: 0.8268 (mmm) cc_final: 0.8007 (mtp) REVERT: L 164 MET cc_start: 0.8019 (mmm) cc_final: 0.7792 (mmm) REVERT: L 221 THR cc_start: 0.6111 (OUTLIER) cc_final: 0.5815 (t) REVERT: L 286 MET cc_start: 0.7778 (pmm) cc_final: 0.7519 (pmm) REVERT: G 164 MET cc_start: 0.8351 (tpt) cc_final: 0.8109 (mmm) REVERT: M 164 MET cc_start: 0.7404 (tpt) cc_final: 0.6985 (mmm) REVERT: M 209 MET cc_start: 0.7485 (tmm) cc_final: 0.7108 (tmm) REVERT: M 286 MET cc_start: 0.7811 (mpp) cc_final: 0.7262 (ptt) REVERT: M 485 MET cc_start: 0.8630 (mmm) cc_final: 0.7799 (mmm) REVERT: H 1 MET cc_start: 0.5524 (ptp) cc_final: 0.5155 (mpp) REVERT: H 7 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: H 164 MET cc_start: 0.8325 (mtp) cc_final: 0.8030 (mmm) REVERT: H 202 MET cc_start: 0.2258 (ptp) cc_final: 0.1951 (ptt) REVERT: H 286 MET cc_start: 0.7924 (pmm) cc_final: 0.7474 (pmm) REVERT: N 103 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8751 (mp) REVERT: N 191 MET cc_start: 0.8080 (mmm) cc_final: 0.7779 (mmm) outliers start: 75 outliers final: 47 residues processed: 236 average time/residue: 0.4638 time to fit residues: 198.4583 Evaluate side-chains 217 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 5.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 507 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 507 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 507 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 92 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 327 optimal weight: 20.0000 chunk 526 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 455 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 397 optimal weight: 30.0000 chunk 370 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 562 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.090894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066881 restraints weight = 204991.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065989 restraints weight = 211890.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.066688 restraints weight = 175954.598| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54922 Z= 0.285 Angle : 0.574 13.956 74368 Z= 0.298 Chirality : 0.042 0.153 9282 Planarity : 0.003 0.030 9674 Dihedral : 3.992 27.864 7662 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 1.51 % Allowed : 13.98 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.10), residues: 7308 helix: 1.99 (0.08), residues: 4004 sheet: 0.01 (0.16), residues: 1232 loop : -0.48 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.004 0.001 HIS H 64 PHE 0.017 0.001 PHE C 7 TYR 0.006 0.001 TYR F 197 ARG 0.005 0.001 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 160 time to evaluate : 5.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5891 (ptp) cc_final: 0.5120 (mpp) REVERT: A 164 MET cc_start: 0.7658 (mmm) cc_final: 0.7301 (mmm) REVERT: A 209 MET cc_start: 0.7523 (tmm) cc_final: 0.7195 (tmm) REVERT: A 286 MET cc_start: 0.7434 (pmm) cc_final: 0.7134 (pmm) REVERT: B 164 MET cc_start: 0.8543 (mmm) cc_final: 0.8050 (mmm) REVERT: B 286 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7877 (pmm) REVERT: C 15 MET cc_start: 0.8778 (mmm) cc_final: 0.8445 (tpp) REVERT: C 103 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8782 (mp) REVERT: C 105 ASN cc_start: 0.9423 (OUTLIER) cc_final: 0.9199 (t0) REVERT: C 164 MET cc_start: 0.8341 (mmm) cc_final: 0.8114 (mmm) REVERT: C 209 MET cc_start: 0.7923 (tmm) cc_final: 0.7638 (tmm) REVERT: C 286 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7677 (pmm) REVERT: C 485 MET cc_start: 0.8347 (mmm) cc_final: 0.8024 (mmt) REVERT: I 164 MET cc_start: 0.8092 (mtp) cc_final: 0.7823 (mmm) REVERT: D 1 MET cc_start: 0.5661 (ptt) cc_final: 0.5017 (mpp) REVERT: D 105 ASN cc_start: 0.9421 (OUTLIER) cc_final: 0.9165 (t0) REVERT: D 164 MET cc_start: 0.8373 (ptm) cc_final: 0.8152 (mtp) REVERT: D 209 MET cc_start: 0.7535 (tmm) cc_final: 0.7239 (tmm) REVERT: D 221 THR cc_start: 0.6407 (OUTLIER) cc_final: 0.6130 (t) REVERT: D 286 MET cc_start: 0.7816 (pmm) cc_final: 0.7604 (pmm) REVERT: J 1 MET cc_start: 0.6202 (mtp) cc_final: 0.5594 (mpp) REVERT: J 164 MET cc_start: 0.7823 (mmm) cc_final: 0.7587 (mmm) REVERT: J 221 THR cc_start: 0.4900 (OUTLIER) cc_final: 0.4587 (t) REVERT: J 286 MET cc_start: 0.7408 (pmm) cc_final: 0.7097 (pmm) REVERT: E 1 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5239 (mpp) REVERT: E 164 MET cc_start: 0.8240 (mmm) cc_final: 0.7680 (mmm) REVERT: E 286 MET cc_start: 0.7753 (pmm) cc_final: 0.7510 (pmm) REVERT: E 511 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8236 (tt) REVERT: K 15 MET cc_start: 0.8757 (mmm) cc_final: 0.8414 (tpp) REVERT: K 164 MET cc_start: 0.8819 (mmm) cc_final: 0.8341 (mmm) REVERT: K 286 MET cc_start: 0.7707 (pmm) cc_final: 0.7395 (pmm) REVERT: F 1 MET cc_start: 0.6884 (mpp) cc_final: 0.6560 (mpp) REVERT: F 164 MET cc_start: 0.8122 (mtp) cc_final: 0.7752 (mmm) REVERT: F 209 MET cc_start: 0.7612 (tmm) cc_final: 0.7324 (tmm) REVERT: L 1 MET cc_start: 0.5652 (ptt) cc_final: 0.5319 (mpp) REVERT: L 103 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8920 (mp) REVERT: L 164 MET cc_start: 0.8123 (mmm) cc_final: 0.7886 (mmm) REVERT: L 209 MET cc_start: 0.7461 (tmm) cc_final: 0.7252 (tmm) REVERT: L 221 THR cc_start: 0.6163 (OUTLIER) cc_final: 0.5876 (t) REVERT: L 286 MET cc_start: 0.7717 (pmm) cc_final: 0.7459 (pmm) REVERT: G 164 MET cc_start: 0.8375 (tpt) cc_final: 0.8149 (mmm) REVERT: G 191 MET cc_start: 0.7662 (mmm) cc_final: 0.7390 (mmm) REVERT: G 209 MET cc_start: 0.7054 (tmm) cc_final: 0.6842 (tmm) REVERT: M 164 MET cc_start: 0.7592 (tpt) cc_final: 0.7163 (mmm) REVERT: M 286 MET cc_start: 0.7687 (mpp) cc_final: 0.7242 (ptp) REVERT: M 485 MET cc_start: 0.8643 (mmm) cc_final: 0.7867 (mmm) REVERT: H 1 MET cc_start: 0.5609 (ptp) cc_final: 0.5172 (mpp) REVERT: H 7 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: H 202 MET cc_start: 0.2327 (ptp) cc_final: 0.1979 (ptt) REVERT: H 286 MET cc_start: 0.7836 (pmm) cc_final: 0.7399 (pmm) REVERT: N 103 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8758 (mp) REVERT: N 105 ASN cc_start: 0.9392 (OUTLIER) cc_final: 0.9164 (t0) REVERT: N 191 MET cc_start: 0.8235 (mmm) cc_final: 0.7984 (mmm) REVERT: N 511 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8227 (tt) outliers start: 89 outliers final: 65 residues processed: 241 average time/residue: 0.4602 time to fit residues: 201.3017 Evaluate side-chains 239 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 159 time to evaluate : 5.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 507 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 507 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 507 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 433 VAL Chi-restraints excluded: chain N residue 507 VAL Chi-restraints excluded: chain N residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 85 optimal weight: 30.0000 chunk 608 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 544 optimal weight: 30.0000 chunk 697 optimal weight: 9.9990 chunk 591 optimal weight: 9.9990 chunk 665 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 645 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 622 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** M 96 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 = 0.4002 r_free = 0.4002 target = 0.104753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072757 restraints weight = 156570.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071535 restraints weight = 144379.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071291 restraints weight = 154628.444| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 54922 Z= 0.298 Angle : 0.715 59.199 74368 Z= 0.407 Chirality : 0.042 0.355 9282 Planarity : 0.004 0.167 9674 Dihedral : 3.997 27.460 7662 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 1.46 % Allowed : 13.98 % Favored : 84.56 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 7308 helix: 1.97 (0.08), residues: 4004 sheet: 0.01 (0.16), residues: 1232 loop : -0.48 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.004 0.001 HIS H 64 PHE 0.016 0.001 PHE C 7 TYR 0.006 0.001 TYR F 197 ARG 0.004 0.000 ARG J 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 159 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5730 (ptp) cc_final: 0.5096 (mpp) REVERT: A 164 MET cc_start: 0.7952 (mmm) cc_final: 0.7663 (mmm) REVERT: A 209 MET cc_start: 0.7989 (tmm) cc_final: 0.7775 (tmm) REVERT: A 286 MET cc_start: 0.7776 (pmm) cc_final: 0.7480 (pmm) REVERT: B 164 MET cc_start: 0.8868 (mmm) cc_final: 0.8195 (mmm) REVERT: B 286 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8166 (pmm) REVERT: C 15 MET cc_start: 0.8755 (mmm) cc_final: 0.8411 (tpp) REVERT: C 103 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8673 (mp) REVERT: C 164 MET cc_start: 0.8531 (mmm) cc_final: 0.8273 (mmm) REVERT: C 209 MET cc_start: 0.8376 (tmm) cc_final: 0.8090 (tmm) REVERT: C 286 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7972 (pmm) REVERT: C 485 MET cc_start: 0.8361 (mmm) cc_final: 0.8053 (mmt) REVERT: I 164 MET cc_start: 0.8488 (mtp) cc_final: 0.7907 (mmm) REVERT: I 286 MET cc_start: 0.7252 (pmm) cc_final: 0.7020 (ptp) REVERT: D 1 MET cc_start: 0.5565 (ptt) cc_final: 0.5031 (mpp) REVERT: D 105 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8860 (t0) REVERT: D 209 MET cc_start: 0.7977 (tmm) cc_final: 0.7636 (tmm) REVERT: D 221 THR cc_start: 0.6397 (OUTLIER) cc_final: 0.6120 (t) REVERT: J 1 MET cc_start: 0.6024 (mtp) cc_final: 0.5473 (mpp) REVERT: J 221 THR cc_start: 0.4845 (OUTLIER) cc_final: 0.4547 (t) REVERT: J 286 MET cc_start: 0.7861 (pmm) cc_final: 0.7573 (pmm) REVERT: E 1 MET cc_start: 0.5542 (OUTLIER) cc_final: 0.5178 (mpp) REVERT: E 164 MET cc_start: 0.8298 (mmm) cc_final: 0.7680 (mmm) REVERT: E 286 MET cc_start: 0.8121 (pmm) cc_final: 0.7917 (pmm) REVERT: E 511 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8332 (tt) REVERT: K 15 MET cc_start: 0.8811 (mmm) cc_final: 0.8378 (tpp) REVERT: K 164 MET cc_start: 0.8969 (mmm) cc_final: 0.8362 (mmm) REVERT: K 286 MET cc_start: 0.8135 (pmm) cc_final: 0.7892 (pmm) REVERT: F 1 MET cc_start: 0.6427 (mpp) cc_final: 0.6128 (mpp) REVERT: F 164 MET cc_start: 0.8638 (mtp) cc_final: 0.8102 (mmm) REVERT: F 209 MET cc_start: 0.8087 (tmm) cc_final: 0.7882 (tmm) REVERT: L 103 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8832 (mp) REVERT: L 164 MET cc_start: 0.8433 (mmm) cc_final: 0.8142 (mmm) REVERT: L 209 MET cc_start: 0.7804 (tmm) cc_final: 0.7563 (tmm) REVERT: L 221 THR cc_start: 0.6148 (OUTLIER) cc_final: 0.5862 (t) REVERT: L 286 MET cc_start: 0.8143 (pmm) cc_final: 0.7916 (pmm) REVERT: G 164 MET cc_start: 0.8649 (tpt) cc_final: 0.8337 (mmm) REVERT: M 164 MET cc_start: 0.7928 (tpt) cc_final: 0.7503 (mmm) REVERT: M 286 MET cc_start: 0.8187 (mpp) cc_final: 0.7962 (pmm) REVERT: M 485 MET cc_start: 0.8707 (mmm) cc_final: 0.7910 (mmm) REVERT: H 1 MET cc_start: 0.5464 (ptp) cc_final: 0.5109 (mpp) REVERT: H 7 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: H 202 MET cc_start: 0.2851 (ptp) cc_final: 0.2618 (ptt) REVERT: N 103 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8715 (mp) REVERT: N 191 MET cc_start: 0.8658 (mmm) cc_final: 0.8316 (mmm) REVERT: N 511 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8355 (tt) outliers start: 86 outliers final: 64 residues processed: 238 average time/residue: 0.4596 time to fit residues: 199.3313 Evaluate side-chains 236 residues out of total 5894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 159 time to evaluate : 4.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 507 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 507 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 507 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 433 VAL Chi-restraints excluded: chain N residue 507 VAL Chi-restraints excluded: chain N residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 509 optimal weight: 8.9990 chunk 425 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 489 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 596 optimal weight: 6.9990 chunk 582 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 605 optimal weight: 40.0000 chunk 481 optimal weight: 5.9990 chunk 564 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 ASN L 105 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.104706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072426 restraints weight = 156814.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.071276 restraints weight = 137735.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070944 restraints weight = 149684.328| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 54922 Z= 0.298 Angle : 0.715 59.199 74368 Z= 0.407 Chirality : 0.042 0.355 9282 Planarity : 0.004 0.167 9674 Dihedral : 3.997 27.460 7662 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 1.34 % Allowed : 14.03 % Favored : 84.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 7308 helix: 1.97 (0.08), residues: 4004 sheet: 0.01 (0.16), residues: 1232 loop : -0.48 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.004 0.001 HIS H 64 PHE 0.016 0.001 PHE C 7 TYR 0.006 0.001 TYR F 197 ARG 0.004 0.000 ARG J 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9720.95 seconds wall clock time: 173 minutes 7.20 seconds (10387.20 seconds total)