Starting phenix.real_space_refine on Wed Sep 25 09:18:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0d_45080/09_2024/9c0d_45080.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0d_45080/09_2024/9c0d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0d_45080/09_2024/9c0d_45080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0d_45080/09_2024/9c0d_45080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0d_45080/09_2024/9c0d_45080.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0d_45080/09_2024/9c0d_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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 24.20, 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: 12.75 Conformation dependent library (CDL) restraints added in 7.4 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: 6.03 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: 26.14 Time building geometry restraints manager: 15.05 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: 0.00 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: 1.020 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: 0.050 Extract box with map and model: 1.710 Check model and map are aligned: 0.300 Set scattering table: 0.400 Process input model: 110.000 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.260 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.770 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 4.845 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: 237.9881 Evaluate side-chains 171 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 4.797 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 4.979 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: 0.3586 (ptp) cc_final: 0.3104 (mpp) REVERT: A 66 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7918 (mt-10) REVERT: A 68 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7243 (mmm) REVERT: A 209 MET cc_start: 0.7921 (tmm) cc_final: 0.7714 (tmm) REVERT: B 7 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: C 1 MET cc_start: 0.6311 (mpp) cc_final: 0.6089 (mpp) REVERT: C 15 MET cc_start: 0.8179 (mmm) cc_final: 0.7805 (tpp) REVERT: C 485 MET cc_start: 0.7588 (mmm) cc_final: 0.7104 (mmt) REVERT: I 7 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: I 191 MET cc_start: 0.8633 (mmm) cc_final: 0.8378 (mmm) REVERT: I 286 MET cc_start: 0.7387 (pmm) cc_final: 0.7079 (pmm) REVERT: D 1 MET cc_start: 0.4352 (ptt) cc_final: 0.3623 (mpp) REVERT: D 7 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: J 15 MET cc_start: 0.7644 (mmm) cc_final: 0.7358 (mmm) REVERT: J 209 MET cc_start: 0.8291 (tmm) cc_final: 0.8040 (tmm) REVERT: E 1 MET cc_start: 0.3982 (OUTLIER) cc_final: 0.2901 (mpp) REVERT: E 164 MET cc_start: 0.7454 (mmm) cc_final: 0.7119 (mmm) REVERT: K 75 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: K 164 MET cc_start: 0.8482 (mmm) cc_final: 0.8134 (mmm) REVERT: K 260 LEU cc_start: 0.8445 (mt) cc_final: 0.8069 (pp) REVERT: K 286 MET cc_start: 0.8005 (pmm) cc_final: 0.7752 (pmm) REVERT: F 164 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7460 (ttp) REVERT: F 209 MET cc_start: 0.7986 (tmm) cc_final: 0.7780 (tmm) REVERT: L 1 MET cc_start: 0.3882 (ptt) cc_final: 0.3676 (mpp) REVERT: L 209 MET cc_start: 0.7910 (tmm) cc_final: 0.7684 (tmm) REVERT: G 15 MET cc_start: 0.8057 (mmm) cc_final: 0.7799 (mmt) REVERT: G 209 MET cc_start: 0.7716 (tmm) cc_final: 0.7402 (tmm) REVERT: G 286 MET cc_start: 0.7838 (pmm) cc_final: 0.7580 (pmm) REVERT: M 286 MET cc_start: 0.8195 (pmm) cc_final: 0.7859 (ptp) REVERT: H 1 MET cc_start: 0.4484 (ptt) cc_final: 0.4098 (mpp) REVERT: H 164 MET cc_start: 0.8423 (ttp) cc_final: 0.7997 (mtp) REVERT: N 511 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6851 (tt) outliers start: 58 outliers final: 20 residues processed: 225 average time/residue: 0.4942 time to fit residues: 201.8471 Evaluate side-chains 190 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 4.862 ------------------------------------------------------------------------------- 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 7 PHE Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain D residue 7 PHE 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 367 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 chunk 550 optimal weight: 4.9990 chunk 450 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 662 optimal weight: 0.5980 chunk 715 optimal weight: 7.9990 chunk 589 optimal weight: 9.9990 chunk 656 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 531 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 ** 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 96 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 F 241 GLN 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 ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 54922 Z= 0.185 Angle : 0.476 9.246 74368 Z= 0.259 Chirality : 0.041 0.151 9282 Planarity : 0.003 0.030 9674 Dihedral : 3.810 26.031 7662 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.35 % Favored : 96.51 % Rotamer: Outliers : 1.26 % Allowed : 10.71 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.10), residues: 7308 helix: 2.13 (0.08), residues: 4032 sheet: -0.18 (0.18), residues: 896 loop : -0.10 (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 C 64 PHE 0.014 0.001 PHE L 7 TYR 0.005 0.001 TYR H 43 ARG 0.003 0.000 ARG A 282 *********************** 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 245 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 171 time to evaluate : 4.938 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: A 66 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 68 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7391 (mmm) REVERT: A 202 MET cc_start: 0.3147 (ptp) cc_final: 0.2752 (ptt) REVERT: A 209 MET cc_start: 0.8056 (tmm) cc_final: 0.7835 (tmm) REVERT: B 7 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: B 15 MET cc_start: 0.8217 (mmm) cc_final: 0.7891 (mmt) REVERT: C 7 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: C 15 MET cc_start: 0.8222 (mmm) cc_final: 0.8014 (tpp) REVERT: C 164 MET cc_start: 0.7712 (mmm) cc_final: 0.7484 (mmm) REVERT: C 485 MET cc_start: 0.7933 (mmm) cc_final: 0.7556 (mmt) REVERT: I 7 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: I 164 MET cc_start: 0.8097 (ttm) cc_final: 0.7556 (mtm) REVERT: I 209 MET cc_start: 0.7667 (tmm) cc_final: 0.7418 (tmm) REVERT: I 286 MET cc_start: 0.7431 (pmm) cc_final: 0.7228 (pmm) REVERT: D 1 MET cc_start: 0.4462 (ptt) cc_final: 0.3797 (mpp) REVERT: D 7 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7025 (m-80) REVERT: D 66 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7962 (mp0) REVERT: D 209 MET cc_start: 0.7799 (tmm) cc_final: 0.7449 (tmm) REVERT: J 209 MET cc_start: 0.8308 (tmm) cc_final: 0.8037 (tmm) REVERT: J 286 MET cc_start: 0.8163 (pmm) cc_final: 0.7954 (pmm) REVERT: E 1 MET cc_start: 0.4464 (OUTLIER) cc_final: 0.3323 (mpp) REVERT: E 164 MET cc_start: 0.7486 (mmm) cc_final: 0.7167 (mmm) REVERT: E 409 MET cc_start: 0.8320 (mmm) cc_final: 0.8094 (mmm) REVERT: E 511 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6598 (tt) REVERT: K 75 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: K 164 MET cc_start: 0.8537 (mmm) cc_final: 0.8151 (mmm) REVERT: K 260 LEU cc_start: 0.8440 (mt) cc_final: 0.8106 (pp) REVERT: K 409 MET cc_start: 0.8458 (mmm) cc_final: 0.8224 (mmm) REVERT: F 1 MET cc_start: 0.6271 (mpp) cc_final: 0.5925 (mpp) REVERT: F 164 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7615 (mtp) REVERT: F 209 MET cc_start: 0.8150 (tmm) cc_final: 0.7941 (tmm) REVERT: L 209 MET cc_start: 0.8022 (tmm) cc_final: 0.7766 (tmm) REVERT: G 164 MET cc_start: 0.7613 (tpt) cc_final: 0.7091 (mmm) REVERT: G 191 MET cc_start: 0.9004 (mmm) cc_final: 0.8646 (mmm) REVERT: G 209 MET cc_start: 0.7723 (tmm) cc_final: 0.7381 (tmm) REVERT: H 1 MET cc_start: 0.4490 (ptt) cc_final: 0.4149 (mpp) REVERT: H 202 MET cc_start: 0.2378 (ptp) cc_final: 0.2064 (ptt) REVERT: N 1 MET cc_start: 0.5966 (ttp) cc_final: 0.5464 (mpp) REVERT: N 191 MET cc_start: 0.8539 (mmm) cc_final: 0.8323 (mmm) REVERT: N 209 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7499 (tmm) REVERT: N 511 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6896 (tt) outliers start: 74 outliers final: 32 residues processed: 237 average time/residue: 0.4805 time to fit residues: 206.3460 Evaluate side-chains 204 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 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 A residue 344 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 194 ASP 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 344 VAL Chi-restraints excluded: chain I residue 7 PHE Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 96 GLN 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 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 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 344 VAL 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 344 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 344 VAL 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 H residue 96 GLN Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 209 MET 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 654 optimal weight: 0.9990 chunk 497 optimal weight: 20.0000 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 444 optimal weight: 6.9990 chunk 664 optimal weight: 9.9990 chunk 703 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 629 optimal weight: 5.9990 chunk 189 optimal weight: 0.2980 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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** C 241 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 241 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 54922 Z= 0.251 Angle : 0.527 9.914 74368 Z= 0.284 Chirality : 0.042 0.198 9282 Planarity : 0.003 0.031 9674 Dihedral : 3.927 26.344 7662 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 1.61 % Allowed : 11.13 % Favored : 87.26 % 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: 1.57 (0.10), residues: 7308 helix: 2.05 (0.08), residues: 4032 sheet: -0.17 (0.18), residues: 896 loop : -0.14 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.005 0.001 HIS M 64 PHE 0.014 0.001 PHE L 7 TYR 0.006 0.001 TYR F 197 ARG 0.004 0.000 ARG J 12 *********************** 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 258 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 163 time to evaluate : 4.918 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 66 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 164 MET cc_start: 0.7082 (mmm) cc_final: 0.6826 (mmm) REVERT: A 209 MET cc_start: 0.8077 (tmm) cc_final: 0.7866 (tmm) REVERT: A 286 MET cc_start: 0.8200 (pmm) cc_final: 0.7997 (pmm) REVERT: B 7 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: B 96 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: C 7 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: C 164 MET cc_start: 0.7919 (mmm) cc_final: 0.7672 (mmm) REVERT: C 191 MET cc_start: 0.8680 (tpp) cc_final: 0.8409 (mmm) REVERT: C 485 MET cc_start: 0.8282 (mmm) cc_final: 0.7969 (mmt) REVERT: I 209 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7472 (tmm) REVERT: D 1 MET cc_start: 0.4324 (ptt) cc_final: 0.4055 (mpp) REVERT: D 7 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: D 209 MET cc_start: 0.7928 (tmm) cc_final: 0.7694 (tmm) REVERT: D 221 THR cc_start: 0.5769 (OUTLIER) cc_final: 0.5539 (t) REVERT: D 511 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6699 (tt) REVERT: J 164 MET cc_start: 0.8380 (mmm) cc_final: 0.8103 (mmm) REVERT: J 209 MET cc_start: 0.8340 (tmm) cc_final: 0.8060 (tmm) REVERT: E 1 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.3619 (mpp) REVERT: E 164 MET cc_start: 0.7713 (mmm) cc_final: 0.7225 (mmm) REVERT: E 409 MET cc_start: 0.7987 (mmm) cc_final: 0.7757 (mmm) REVERT: K 75 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6627 (tm-30) REVERT: K 96 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: K 164 MET cc_start: 0.8651 (mmm) cc_final: 0.8229 (mmm) REVERT: K 260 LEU cc_start: 0.8483 (mt) cc_final: 0.8133 (pp) REVERT: F 1 MET cc_start: 0.6711 (mpp) cc_final: 0.6432 (mpp) REVERT: F 164 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7681 (mtp) REVERT: L 66 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8050 (mp0) REVERT: L 209 MET cc_start: 0.8094 (tmm) cc_final: 0.7819 (tmm) REVERT: L 511 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6615 (tt) REVERT: G 164 MET cc_start: 0.7893 (tpt) cc_final: 0.7457 (mmm) REVERT: G 209 MET cc_start: 0.7852 (tmm) cc_final: 0.7499 (tmm) REVERT: M 4 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: M 209 MET cc_start: 0.7975 (tmm) cc_final: 0.7768 (tmm) REVERT: H 66 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8017 (mp0) REVERT: H 96 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: H 164 MET cc_start: 0.8555 (mtp) cc_final: 0.8048 (mmm) REVERT: H 209 MET cc_start: 0.7904 (tmm) cc_final: 0.7593 (tmm) REVERT: H 286 MET cc_start: 0.8359 (pmm) cc_final: 0.8152 (pmm) REVERT: N 1 MET cc_start: 0.6248 (ttp) cc_final: 0.5628 (mpp) REVERT: N 209 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7630 (tmm) REVERT: N 511 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6921 (tt) outliers start: 95 outliers final: 40 residues processed: 246 average time/residue: 0.4770 time to fit residues: 213.1162 Evaluate side-chains 214 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 158 time to evaluate : 4.848 ------------------------------------------------------------------------------- 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 B residue 1 MET Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 96 GLN 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 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 209 MET Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain D residue 7 PHE 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 D residue 511 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 202 MET 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 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 106 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 4 GLU 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 433 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 194 ASP Chi-restraints excluded: chain N residue 209 MET Chi-restraints excluded: chain N residue 344 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 586 optimal weight: 8.9990 chunk 399 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 523 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 600 optimal weight: 6.9990 chunk 486 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 0.0770 chunk 631 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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 ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN F 105 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 54922 Z= 0.242 Angle : 0.506 8.876 74368 Z= 0.274 Chirality : 0.041 0.148 9282 Planarity : 0.003 0.031 9674 Dihedral : 3.918 25.674 7662 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 1.61 % Allowed : 11.66 % Favored : 86.73 % 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: 2.01 (0.08), residues: 4032 sheet: 0.03 (0.17), residues: 1008 loop : -0.43 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.004 0.001 HIS I 64 PHE 0.013 0.001 PHE L 7 TYR 0.007 0.001 TYR I 197 ARG 0.005 0.000 ARG M 282 *********************** 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 263 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 168 time to evaluate : 4.896 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: A 66 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 209 MET cc_start: 0.8086 (tmm) cc_final: 0.7859 (tmm) REVERT: A 286 MET cc_start: 0.8253 (pmm) cc_final: 0.8045 (pmm) REVERT: B 7 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: B 164 MET cc_start: 0.8742 (mtp) cc_final: 0.8127 (mmm) REVERT: C 7 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: C 164 MET cc_start: 0.8155 (mmm) cc_final: 0.7919 (mmm) REVERT: C 286 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8156 (pmm) REVERT: I 7 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: I 164 MET cc_start: 0.8336 (mtp) cc_final: 0.7824 (mmm) REVERT: I 209 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7412 (tmm) REVERT: D 1 MET cc_start: 0.4320 (ptt) cc_final: 0.4079 (mpp) REVERT: D 7 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: D 164 MET cc_start: 0.8292 (ptm) cc_final: 0.8001 (mtp) REVERT: D 209 MET cc_start: 0.7945 (tmm) cc_final: 0.7722 (tmm) REVERT: J 209 MET cc_start: 0.8430 (tmm) cc_final: 0.8164 (tmm) REVERT: J 286 MET cc_start: 0.8370 (pmm) cc_final: 0.8123 (pmm) REVERT: E 1 MET cc_start: 0.4925 (OUTLIER) cc_final: 0.4017 (mpp) REVERT: E 164 MET cc_start: 0.7833 (mmm) cc_final: 0.7271 (mmm) REVERT: E 511 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6674 (tt) REVERT: K 75 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: K 164 MET cc_start: 0.8895 (mmm) cc_final: 0.8372 (mmm) REVERT: K 260 LEU cc_start: 0.8466 (mt) cc_final: 0.8100 (pp) REVERT: F 1 MET cc_start: 0.6605 (mpp) cc_final: 0.6368 (mpp) REVERT: F 164 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7795 (mtp) REVERT: L 66 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8088 (mp0) REVERT: L 209 MET cc_start: 0.8098 (tmm) cc_final: 0.7820 (tmm) REVERT: L 221 THR cc_start: 0.5664 (OUTLIER) cc_final: 0.5414 (t) REVERT: G 15 MET cc_start: 0.7900 (mmm) cc_final: 0.7374 (mtt) REVERT: G 164 MET cc_start: 0.8246 (tpt) cc_final: 0.7913 (mmm) REVERT: G 209 MET cc_start: 0.7854 (tmm) cc_final: 0.7510 (tmm) REVERT: M 164 MET cc_start: 0.7719 (tpt) cc_final: 0.7249 (mmm) REVERT: H 7 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: H 96 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: H 164 MET cc_start: 0.8506 (mtp) cc_final: 0.7744 (mmm) REVERT: H 202 MET cc_start: 0.2764 (ptp) cc_final: 0.2357 (ptt) REVERT: H 209 MET cc_start: 0.8008 (tmm) cc_final: 0.7798 (tmm) REVERT: N 1 MET cc_start: 0.6347 (ttp) cc_final: 0.5572 (mpp) REVERT: N 209 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7650 (tmm) REVERT: N 511 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6959 (tt) outliers start: 95 outliers final: 51 residues processed: 251 average time/residue: 0.4723 time to fit residues: 215.4387 Evaluate side-chains 225 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 159 time to evaluate : 4.856 ------------------------------------------------------------------------------- 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 7 PHE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 29 THR 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 7 PHE Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain D residue 7 PHE 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 202 MET 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 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 344 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 113 LEU 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 344 VAL Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 508 SER 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 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 96 GLN Chi-restraints excluded: chain H residue 103 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 20.0000 chunk 633 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 413 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 704 optimal weight: 8.9990 chunk 584 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 369 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54922 Z= 0.177 Angle : 0.481 11.173 74368 Z= 0.257 Chirality : 0.040 0.141 9282 Planarity : 0.003 0.028 9674 Dihedral : 3.852 25.004 7662 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 1.41 % Allowed : 12.61 % Favored : 85.99 % 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: 1.55 (0.10), residues: 7308 helix: 2.11 (0.08), residues: 4032 sheet: 0.06 (0.17), residues: 1008 loop : -0.45 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 482 HIS 0.003 0.001 HIS B 64 PHE 0.012 0.001 PHE L 7 TYR 0.006 0.001 TYR J 43 ARG 0.005 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 252 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 169 time to evaluate : 4.891 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 66 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7801 (mp0) REVERT: A 209 MET cc_start: 0.8105 (tmm) cc_final: 0.7884 (tmm) REVERT: B 7 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 164 MET cc_start: 0.8825 (mtp) cc_final: 0.8285 (mmm) REVERT: C 7 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: C 164 MET cc_start: 0.8269 (mmm) cc_final: 0.8037 (mmm) REVERT: C 286 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8198 (pmm) REVERT: I 7 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: I 164 MET cc_start: 0.8330 (mtp) cc_final: 0.7759 (mmm) REVERT: I 209 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7416 (tmm) REVERT: I 286 MET cc_start: 0.7750 (pmm) cc_final: 0.7492 (pmm) REVERT: D 1 MET cc_start: 0.4436 (ptt) cc_final: 0.4119 (mpp) REVERT: D 7 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: D 209 MET cc_start: 0.7953 (tmm) cc_final: 0.7715 (tmm) REVERT: D 221 THR cc_start: 0.6054 (OUTLIER) cc_final: 0.5832 (t) REVERT: J 164 MET cc_start: 0.8376 (mmm) cc_final: 0.8105 (mmm) REVERT: J 209 MET cc_start: 0.8415 (tmm) cc_final: 0.8146 (tmm) REVERT: J 286 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8196 (pmm) REVERT: E 1 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.3946 (mpp) REVERT: E 164 MET cc_start: 0.7875 (mmm) cc_final: 0.7287 (mmm) REVERT: E 511 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6717 (tt) REVERT: K 75 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: K 96 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: K 164 MET cc_start: 0.8901 (mmm) cc_final: 0.8432 (mmm) REVERT: K 260 LEU cc_start: 0.8477 (mt) cc_final: 0.8100 (pp) REVERT: F 1 MET cc_start: 0.6304 (mpp) cc_final: 0.6091 (mpp) REVERT: L 66 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8083 (mp0) REVERT: L 164 MET cc_start: 0.7635 (mmm) cc_final: 0.7323 (mmm) REVERT: L 209 MET cc_start: 0.8089 (tmm) cc_final: 0.7815 (tmm) REVERT: L 221 THR cc_start: 0.5654 (OUTLIER) cc_final: 0.5409 (t) REVERT: L 286 MET cc_start: 0.8193 (pmm) cc_final: 0.7973 (pmm) REVERT: G 15 MET cc_start: 0.7871 (mmm) cc_final: 0.7318 (mtt) REVERT: G 164 MET cc_start: 0.8329 (tpt) cc_final: 0.8037 (mmm) REVERT: G 209 MET cc_start: 0.7862 (tmm) cc_final: 0.7512 (tmm) REVERT: G 286 MET cc_start: 0.7826 (pmm) cc_final: 0.7471 (pmm) REVERT: M 4 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7805 (tp30) REVERT: M 164 MET cc_start: 0.7887 (tpt) cc_final: 0.7471 (mmm) REVERT: H 7 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: H 66 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7949 (mp0) REVERT: H 96 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: H 164 MET cc_start: 0.8588 (mtp) cc_final: 0.7878 (mmm) REVERT: H 202 MET cc_start: 0.2624 (ptp) cc_final: 0.2296 (ptt) REVERT: H 209 MET cc_start: 0.8130 (tmm) cc_final: 0.7886 (tmm) REVERT: N 1 MET cc_start: 0.6173 (ttp) cc_final: 0.5477 (mpp) REVERT: N 191 MET cc_start: 0.9082 (mmm) cc_final: 0.8707 (mmm) REVERT: N 209 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7704 (tmm) REVERT: N 511 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6955 (tt) outliers start: 83 outliers final: 45 residues processed: 240 average time/residue: 0.4651 time to fit residues: 202.8971 Evaluate side-chains 225 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 162 time to evaluate : 4.845 ------------------------------------------------------------------------------- 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 7 PHE 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 286 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain I residue 7 PHE 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 209 MET Chi-restraints excluded: chain I residue 507 VAL Chi-restraints excluded: chain D residue 7 PHE 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 246 LEU Chi-restraints excluded: chain J residue 286 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 191 MET 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 96 GLN Chi-restraints excluded: chain F residue 29 THR 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 G residue 344 VAL Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 4 GLU 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 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 96 GLN 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 194 ASP Chi-restraints excluded: chain N residue 209 MET Chi-restraints excluded: chain N residue 344 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 679 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 401 optimal weight: 30.0000 chunk 514 optimal weight: 0.7980 chunk 398 optimal weight: 8.9990 chunk 592 optimal weight: 5.9990 chunk 393 optimal weight: 6.9990 chunk 701 optimal weight: 20.0000 chunk 439 optimal weight: 10.0000 chunk 427 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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** ** G 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54922 Z= 0.223 Angle : 0.513 13.137 74368 Z= 0.271 Chirality : 0.041 0.207 9282 Planarity : 0.003 0.030 9674 Dihedral : 3.862 24.842 7662 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 1.78 % Allowed : 12.72 % Favored : 85.49 % 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: 1.53 (0.10), residues: 7308 helix: 2.10 (0.08), residues: 4018 sheet: 0.02 (0.16), residues: 1232 loop : -0.49 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.003 0.001 HIS I 64 PHE 0.012 0.001 PHE G 7 TYR 0.006 0.001 TYR I 197 ARG 0.005 0.000 ARG K 282 *********************** 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 272 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 167 time to evaluate : 4.883 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 209 MET cc_start: 0.8123 (tmm) cc_final: 0.7899 (tmm) REVERT: B 7 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: B 164 MET cc_start: 0.8865 (mtp) cc_final: 0.8312 (mmm) REVERT: B 286 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (pmm) REVERT: C 103 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7736 (mp) REVERT: C 164 MET cc_start: 0.8400 (mmm) cc_final: 0.8132 (mmm) REVERT: C 286 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8201 (pmm) REVERT: C 485 MET cc_start: 0.8425 (mmm) cc_final: 0.7778 (mmt) REVERT: I 7 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: I 164 MET cc_start: 0.8385 (mtp) cc_final: 0.7754 (mmm) REVERT: I 191 MET cc_start: 0.8773 (mmm) cc_final: 0.8550 (mmm) REVERT: I 286 MET cc_start: 0.7760 (pmm) cc_final: 0.7305 (ptp) REVERT: D 1 MET cc_start: 0.4156 (ptt) cc_final: 0.3938 (mpp) REVERT: D 7 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: D 209 MET cc_start: 0.8004 (tmm) cc_final: 0.7764 (tmm) REVERT: D 221 THR cc_start: 0.5889 (OUTLIER) cc_final: 0.5666 (t) REVERT: J 1 MET cc_start: 0.5299 (mtp) cc_final: 0.4682 (mpp) REVERT: J 209 MET cc_start: 0.8427 (tmm) cc_final: 0.8176 (tmm) REVERT: J 286 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8204 (pmm) REVERT: E 1 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.3953 (mpp) REVERT: E 164 MET cc_start: 0.8034 (mmm) cc_final: 0.7452 (mmm) REVERT: E 511 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6831 (tt) REVERT: K 96 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: K 164 MET cc_start: 0.8932 (mmm) cc_final: 0.8455 (mmm) REVERT: K 260 LEU cc_start: 0.8504 (mt) cc_final: 0.8144 (pp) REVERT: L 209 MET cc_start: 0.8116 (tmm) cc_final: 0.7839 (tmm) REVERT: L 221 THR cc_start: 0.5842 (OUTLIER) cc_final: 0.5607 (t) REVERT: G 15 MET cc_start: 0.7842 (mmm) cc_final: 0.7342 (mtt) REVERT: G 66 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8222 (mp0) REVERT: G 164 MET cc_start: 0.8470 (tpt) cc_final: 0.8226 (mmm) REVERT: G 209 MET cc_start: 0.7901 (tmm) cc_final: 0.7577 (tmm) REVERT: G 286 MET cc_start: 0.7790 (pmm) cc_final: 0.7579 (ptp) REVERT: M 4 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: M 164 MET cc_start: 0.8267 (tpt) cc_final: 0.7932 (mmm) REVERT: H 7 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: H 96 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: H 164 MET cc_start: 0.8688 (mtp) cc_final: 0.8037 (mmm) REVERT: H 202 MET cc_start: 0.2676 (ptp) cc_final: 0.2429 (ptt) REVERT: H 209 MET cc_start: 0.8142 (tmm) cc_final: 0.7925 (tmm) REVERT: H 286 MET cc_start: 0.8350 (pmm) cc_final: 0.8054 (pmm) REVERT: N 1 MET cc_start: 0.6320 (ttp) cc_final: 0.5640 (mpp) REVERT: N 66 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8097 (mp0) REVERT: N 209 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7707 (tmm) REVERT: N 511 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6954 (tt) outliers start: 105 outliers final: 61 residues processed: 262 average time/residue: 0.4546 time to fit residues: 217.3539 Evaluate side-chains 241 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 163 time to evaluate : 4.752 ------------------------------------------------------------------------------- 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 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 7 PHE 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 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 7 PHE 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 D residue 7 PHE 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 246 LEU Chi-restraints excluded: chain J residue 286 MET 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 25 THR Chi-restraints excluded: chain K residue 29 THR 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 106 VAL Chi-restraints excluded: chain F residue 433 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 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 4 GLU 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 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 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 209 MET Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 507 VAL Chi-restraints excluded: chain N residue 511 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 0.6980 chunk 280 optimal weight: 30.0000 chunk 419 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 137 optimal weight: 40.0000 chunk 135 optimal weight: 50.0000 chunk 446 optimal weight: 3.9990 chunk 478 optimal weight: 10.0000 chunk 346 optimal weight: 30.0000 chunk 65 optimal weight: 0.0870 chunk 551 optimal weight: 20.0000 overall best weight: 3.9564 ------------------------------------------------------------------------------- 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** D 105 ASN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3113 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= 0.212 Angle : 0.513 13.654 74368 Z= 0.268 Chirality : 0.041 0.164 9282 Planarity : 0.003 0.028 9674 Dihedral : 3.877 24.828 7662 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 1.49 % Allowed : 13.20 % Favored : 85.31 % 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: 1.52 (0.10), residues: 7308 helix: 2.11 (0.08), residues: 4018 sheet: 0.04 (0.15), residues: 1232 loop : -0.53 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.003 0.001 HIS G 64 PHE 0.014 0.001 PHE C 7 TYR 0.006 0.001 TYR F 201 ARG 0.005 0.000 ARG D 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 259 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 171 time to evaluate : 4.885 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 209 MET cc_start: 0.8125 (tmm) cc_final: 0.7898 (tmm) REVERT: B 7 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: B 164 MET cc_start: 0.8895 (mtp) cc_final: 0.8333 (mmm) REVERT: B 286 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8314 (pmm) REVERT: C 103 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7665 (mp) REVERT: C 164 MET cc_start: 0.8498 (mmm) cc_final: 0.8212 (mmm) REVERT: C 286 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8170 (pmm) REVERT: I 7 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: I 164 MET cc_start: 0.8534 (mtp) cc_final: 0.7859 (mmm) REVERT: I 286 MET cc_start: 0.7732 (pmm) cc_final: 0.7303 (ptp) REVERT: D 1 MET cc_start: 0.4141 (ptt) cc_final: 0.3936 (mpp) REVERT: D 7 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: D 209 MET cc_start: 0.7999 (tmm) cc_final: 0.7777 (tmm) REVERT: D 221 THR cc_start: 0.5754 (OUTLIER) cc_final: 0.5538 (t) REVERT: D 286 MET cc_start: 0.8135 (pmm) cc_final: 0.7765 (pmm) REVERT: J 1 MET cc_start: 0.5370 (mtp) cc_final: 0.4747 (mpp) REVERT: J 209 MET cc_start: 0.8456 (tmm) cc_final: 0.8229 (tmm) REVERT: J 286 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8159 (pmm) REVERT: E 1 MET cc_start: 0.5320 (OUTLIER) cc_final: 0.4416 (mpp) REVERT: E 164 MET cc_start: 0.8165 (mmm) cc_final: 0.7583 (mmm) REVERT: E 511 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6873 (tt) REVERT: K 96 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: K 164 MET cc_start: 0.8931 (mmm) cc_final: 0.8357 (mmm) REVERT: K 260 LEU cc_start: 0.8515 (mt) cc_final: 0.8157 (pp) REVERT: F 164 MET cc_start: 0.8498 (mtp) cc_final: 0.7909 (mmm) REVERT: L 209 MET cc_start: 0.8124 (tmm) cc_final: 0.7849 (tmm) REVERT: L 221 THR cc_start: 0.5847 (OUTLIER) cc_final: 0.5617 (t) REVERT: L 286 MET cc_start: 0.8221 (pmm) cc_final: 0.8016 (pmm) REVERT: G 15 MET cc_start: 0.7841 (mmm) cc_final: 0.7354 (mtt) REVERT: G 66 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8235 (mp0) REVERT: G 164 MET cc_start: 0.8562 (tpt) cc_final: 0.8312 (mmm) REVERT: G 209 MET cc_start: 0.7991 (tmm) cc_final: 0.7718 (tmm) REVERT: M 4 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7920 (tp30) REVERT: M 164 MET cc_start: 0.8397 (tpt) cc_final: 0.8082 (mmm) REVERT: H 7 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: H 96 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: H 164 MET cc_start: 0.8718 (mtp) cc_final: 0.8068 (mmm) REVERT: H 209 MET cc_start: 0.8137 (tmm) cc_final: 0.7914 (tmm) REVERT: H 286 MET cc_start: 0.8371 (pmm) cc_final: 0.8079 (pmm) REVERT: N 1 MET cc_start: 0.6367 (ttp) cc_final: 0.5773 (mpp) REVERT: N 66 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8146 (mp0) REVERT: N 191 MET cc_start: 0.9046 (mmm) cc_final: 0.8647 (mmm) REVERT: N 209 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7718 (tmm) outliers start: 88 outliers final: 57 residues processed: 250 average time/residue: 0.4517 time to fit residues: 206.4538 Evaluate side-chains 236 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 163 time to evaluate : 4.802 ------------------------------------------------------------------------------- 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 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 7 PHE 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 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 7 PHE 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 D residue 7 PHE 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 106 VAL Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 286 MET 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 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 433 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 L residue 433 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 4 GLU 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 507 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 96 GLN 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 209 MET Chi-restraints excluded: chain N residue 344 VAL 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 638 optimal weight: 10.0000 chunk 672 optimal weight: 10.0000 chunk 613 optimal weight: 5.9990 chunk 653 optimal weight: 7.9990 chunk 393 optimal weight: 0.0370 chunk 284 optimal weight: 2.9990 chunk 513 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 590 optimal weight: 20.0000 chunk 618 optimal weight: 5.9990 chunk 651 optimal weight: 20.0000 overall best weight: 3.2064 ------------------------------------------------------------------------------- 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** D 105 ASN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54922 Z= 0.185 Angle : 0.503 14.115 74368 Z= 0.262 Chirality : 0.040 0.150 9282 Planarity : 0.003 0.028 9674 Dihedral : 3.833 24.501 7662 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.53 % Allowed : 13.34 % Favored : 85.14 % 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: 1.55 (0.10), residues: 7308 helix: 2.14 (0.08), residues: 4018 sheet: 0.08 (0.16), residues: 1232 loop : -0.56 (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 H 64 PHE 0.015 0.001 PHE C 7 TYR 0.007 0.001 TYR M 197 ARG 0.004 0.000 ARG A 282 *********************** 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 255 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 165 time to evaluate : 4.918 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 209 MET cc_start: 0.8118 (tmm) cc_final: 0.7887 (tmm) REVERT: A 286 MET cc_start: 0.8059 (pmm) cc_final: 0.7821 (pmm) REVERT: B 7 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: B 66 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8008 (mp0) REVERT: B 164 MET cc_start: 0.8924 (mtp) cc_final: 0.8407 (mmm) REVERT: B 286 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8257 (pmm) REVERT: C 103 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7650 (mp) REVERT: C 164 MET cc_start: 0.8530 (mmm) cc_final: 0.8241 (mmm) REVERT: C 286 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8168 (pmm) REVERT: I 7 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: I 164 MET cc_start: 0.8611 (mtp) cc_final: 0.7940 (mmm) REVERT: I 286 MET cc_start: 0.7804 (pmm) cc_final: 0.7389 (ptp) REVERT: D 1 MET cc_start: 0.4282 (ptt) cc_final: 0.4043 (mpp) REVERT: D 7 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: D 209 MET cc_start: 0.7991 (tmm) cc_final: 0.7765 (tmm) REVERT: D 221 THR cc_start: 0.5807 (OUTLIER) cc_final: 0.5593 (t) REVERT: D 286 MET cc_start: 0.8158 (pmm) cc_final: 0.7788 (pmm) REVERT: J 1 MET cc_start: 0.5315 (mtp) cc_final: 0.4729 (mpp) REVERT: J 286 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8149 (pmm) REVERT: E 1 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.4400 (mpp) REVERT: E 164 MET cc_start: 0.8218 (mmm) cc_final: 0.7793 (mmm) REVERT: E 511 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6869 (tt) REVERT: K 96 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: K 164 MET cc_start: 0.8961 (mmm) cc_final: 0.8389 (mmm) REVERT: K 260 LEU cc_start: 0.8524 (mt) cc_final: 0.8165 (pp) REVERT: F 164 MET cc_start: 0.8555 (mtp) cc_final: 0.7839 (mmm) REVERT: L 209 MET cc_start: 0.8132 (tmm) cc_final: 0.7931 (tmm) REVERT: L 221 THR cc_start: 0.5841 (OUTLIER) cc_final: 0.5614 (t) REVERT: L 286 MET cc_start: 0.8208 (pmm) cc_final: 0.7999 (pmm) REVERT: G 15 MET cc_start: 0.7834 (mmm) cc_final: 0.7361 (mtt) REVERT: G 66 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8202 (mp0) REVERT: G 164 MET cc_start: 0.8614 (tpt) cc_final: 0.8358 (mmm) REVERT: G 209 MET cc_start: 0.8015 (tmm) cc_final: 0.7747 (tmm) REVERT: M 4 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: M 164 MET cc_start: 0.8457 (tpt) cc_final: 0.8221 (mmm) REVERT: H 7 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6743 (m-80) REVERT: H 164 MET cc_start: 0.8761 (mtp) cc_final: 0.8156 (mmm) REVERT: H 286 MET cc_start: 0.8366 (pmm) cc_final: 0.8045 (pmm) REVERT: N 1 MET cc_start: 0.6361 (ttp) cc_final: 0.5764 (mpp) REVERT: N 66 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8112 (mp0) REVERT: N 191 MET cc_start: 0.9040 (mmm) cc_final: 0.8612 (mmm) REVERT: N 209 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7707 (tmm) REVERT: N 511 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6927 (tt) outliers start: 90 outliers final: 58 residues processed: 245 average time/residue: 0.4537 time to fit residues: 204.5010 Evaluate side-chains 240 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 166 time to evaluate : 4.848 ------------------------------------------------------------------------------- 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 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 7 PHE 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 106 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain I residue 7 PHE 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 D residue 7 PHE 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 246 LEU Chi-restraints excluded: chain J residue 286 MET 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 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 96 GLN 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 433 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 105 ASN 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 99 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain M residue 4 GLU 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 507 VAL Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 26 VAL 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 209 MET 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 429 optimal weight: 9.9990 chunk 691 optimal weight: 10.0000 chunk 422 optimal weight: 0.7980 chunk 328 optimal weight: 6.9990 chunk 480 optimal weight: 0.9990 chunk 725 optimal weight: 2.9990 chunk 667 optimal weight: 8.9990 chunk 577 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 446 optimal weight: 0.6980 chunk 354 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 105 ASN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 54922 Z= 0.131 Angle : 0.494 13.478 74368 Z= 0.254 Chirality : 0.040 0.162 9282 Planarity : 0.003 0.026 9674 Dihedral : 3.775 23.294 7660 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 0.85 % Allowed : 14.03 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7308 helix: 2.21 (0.08), residues: 4004 sheet: 0.13 (0.15), residues: 1232 loop : -0.60 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 482 HIS 0.003 0.001 HIS A 64 PHE 0.020 0.001 PHE M 7 TYR 0.007 0.001 TYR I 43 ARG 0.003 0.000 ARG D 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 221 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 4.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8109 (tmm) cc_final: 0.7873 (tmm) REVERT: A 286 MET cc_start: 0.8082 (pmm) cc_final: 0.7843 (pmm) REVERT: B 7 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: B 15 MET cc_start: 0.8025 (mmm) cc_final: 0.7679 (mmm) REVERT: B 66 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8020 (mp0) REVERT: B 164 MET cc_start: 0.8893 (mtp) cc_final: 0.8420 (mmm) REVERT: B 286 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8282 (pmm) REVERT: C 164 MET cc_start: 0.8502 (mmm) cc_final: 0.8207 (mmm) REVERT: C 286 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8153 (pmm) REVERT: C 485 MET cc_start: 0.8294 (mmm) cc_final: 0.7379 (mmt) REVERT: I 7 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: I 164 MET cc_start: 0.8639 (mtp) cc_final: 0.7983 (mmm) REVERT: I 286 MET cc_start: 0.7829 (pmm) cc_final: 0.7460 (ptp) REVERT: D 1 MET cc_start: 0.4260 (ptt) cc_final: 0.4047 (mpp) REVERT: D 7 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: D 66 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7941 (mp0) REVERT: D 191 MET cc_start: 0.8869 (tpp) cc_final: 0.8087 (mmm) REVERT: D 209 MET cc_start: 0.7986 (tmm) cc_final: 0.7752 (tmm) REVERT: D 286 MET cc_start: 0.8174 (pmm) cc_final: 0.7822 (pmm) REVERT: J 1 MET cc_start: 0.5268 (mtp) cc_final: 0.4706 (mpp) REVERT: J 164 MET cc_start: 0.8048 (mmm) cc_final: 0.7781 (mmm) REVERT: J 286 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8144 (pmm) REVERT: E 1 MET cc_start: 0.5387 (ptm) cc_final: 0.4512 (mpp) REVERT: E 164 MET cc_start: 0.8232 (mmm) cc_final: 0.7809 (mmm) REVERT: E 191 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: E 511 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6853 (tt) REVERT: K 164 MET cc_start: 0.8966 (mmm) cc_final: 0.8397 (mmm) REVERT: K 260 LEU cc_start: 0.8524 (mt) cc_final: 0.8165 (pp) REVERT: F 164 MET cc_start: 0.8620 (mtp) cc_final: 0.7965 (mmm) REVERT: F 485 MET cc_start: 0.8646 (mmm) cc_final: 0.8442 (mmm) REVERT: L 66 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8094 (mp0) REVERT: L 209 MET cc_start: 0.8124 (tmm) cc_final: 0.7921 (tmm) REVERT: L 221 THR cc_start: 0.5840 (OUTLIER) cc_final: 0.5607 (t) REVERT: L 286 MET cc_start: 0.8211 (pmm) cc_final: 0.7996 (pmm) REVERT: G 15 MET cc_start: 0.7790 (mmm) cc_final: 0.7314 (mtt) REVERT: G 66 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8189 (mp0) REVERT: G 164 MET cc_start: 0.8625 (tpt) cc_final: 0.8366 (mmm) REVERT: G 209 MET cc_start: 0.8001 (tmm) cc_final: 0.7748 (tmm) REVERT: M 164 MET cc_start: 0.8454 (tpt) cc_final: 0.8205 (mmm) REVERT: H 7 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: H 66 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7970 (mp0) REVERT: H 164 MET cc_start: 0.8790 (mtp) cc_final: 0.8167 (mmm) REVERT: H 202 MET cc_start: 0.2190 (ptp) cc_final: 0.1718 (ptt) REVERT: H 286 MET cc_start: 0.8360 (pmm) cc_final: 0.8050 (pmm) REVERT: N 1 MET cc_start: 0.6304 (ttp) cc_final: 0.5911 (mtt) REVERT: N 191 MET cc_start: 0.9069 (mmm) cc_final: 0.8638 (mmm) REVERT: N 209 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: N 286 MET cc_start: 0.8049 (pmm) cc_final: 0.7668 (pmm) REVERT: N 511 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6922 (tt) outliers start: 50 outliers final: 31 residues processed: 213 average time/residue: 0.4696 time to fit residues: 182.0398 Evaluate side-chains 210 residues out of total 5894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 4.937 ------------------------------------------------------------------------------- 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 68 MET Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain B residue 7 PHE 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 C residue 7 PHE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain I residue 7 PHE 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 D residue 7 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 286 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 511 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 433 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 221 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain H residue 25 THR 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 194 ASP Chi-restraints excluded: chain N residue 209 MET 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 458 optimal weight: 2.9990 chunk 615 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 532 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 160 optimal weight: 0.0980 chunk 578 optimal weight: 1.9990 chunk 242 optimal weight: 30.0000 chunk 593 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 106 optimal weight: 8.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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** C 105 ASN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4000 r_free = 0.4000 target = 0.092799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.068653 restraints weight = 206357.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.067968 restraints weight = 206781.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.068430 restraints weight = 146575.408| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 54922 Z= 0.163 Angle : 0.498 12.156 74368 Z= 0.256 Chirality : 0.040 0.152 9282 Planarity : 0.003 0.027 9674 Dihedral : 3.734 24.863 7660 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 0.97 % Allowed : 14.00 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 7308 helix: 2.24 (0.08), residues: 4004 sheet: -0.07 (0.16), residues: 1092 loop : -0.63 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.006 0.001 HIS N 64 PHE 0.016 0.001 PHE M 7 TYR 0.008 0.001 TYR J 197 ARG 0.003 0.000 ARG D 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6089.65 seconds wall clock time: 118 minutes 27.49 seconds (7107.49 seconds total)