Starting phenix.real_space_refine on Sun Jun 29 05:39:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e96_47775/06_2025/9e96_47775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e96_47775/06_2025/9e96_47775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e96_47775/06_2025/9e96_47775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e96_47775/06_2025/9e96_47775.map" model { file = "/net/cci-nas-00/data/ceres_data/9e96_47775/06_2025/9e96_47775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e96_47775/06_2025/9e96_47775.cif" } resolution = 4.05 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= 0.001 sd= 0.072 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 196 5.16 5 C 21500 2.51 5 N 5864 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33952 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "F" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "G" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "H" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "I" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "J" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "K" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "M" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "N" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3322 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "O" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3188 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "P" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "Q" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "R" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Time building chain proxies: 19.55, per 1000 atoms: 0.58 Number of scatterers: 33952 At special positions: 0 Unit cell: (163.17, 169.83, 198.69, 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 196 16.00 O 6392 8.00 N 5864 7.00 C 21500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.02 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.04 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 124 " distance=2.02 Simple disulfide: pdb=" SG CYS G 91 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 226 " distance=2.04 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 85 " - pdb=" SG CYS H 91 " distance=2.02 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.02 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.04 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 124 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.02 Simple disulfide: pdb=" SG CYS L 85 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS N 49 " - pdb=" SG CYS N 114 " distance=2.03 Simple disulfide: pdb=" SG CYS N 62 " - pdb=" SG CYS N 94 " distance=2.03 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 259 " - pdb=" SG CYS N 271 " distance=2.03 Simple disulfide: pdb=" SG CYS N 301 " - pdb=" SG CYS N 376 " distance=2.02 Simple disulfide: pdb=" SG CYS N 306 " - pdb=" SG CYS N 380 " distance=2.03 Simple disulfide: pdb=" SG CYS N 328 " - pdb=" SG CYS N 370 " distance=2.03 Simple disulfide: pdb=" SG CYS O 16 " - pdb=" SG CYS O 124 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 25 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 105 " distance=2.02 Simple disulfide: pdb=" SG CYS O 152 " - pdb=" SG CYS O 266 " distance=2.03 Simple disulfide: pdb=" SG CYS O 201 " - pdb=" SG CYS O 226 " distance=2.03 Simple disulfide: pdb=" SG CYS O 203 " - pdb=" SG CYS O 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 85 " - pdb=" SG CYS P 91 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 85 " - pdb=" SG CYS Q 91 " distance=2.03 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: 8.70 Conformation dependent library (CDL) restraints added in 4.2 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8136 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 98 sheets defined 13.8% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 398 through 402 removed outlier: 4.084A pdb=" N VAL A 402 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.741A pdb=" N ALA A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.697A pdb=" N ILE B 357 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 402 removed outlier: 3.989A pdb=" N LYS B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 3.793A pdb=" N LEU B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'F' and resid 112 through 116 removed outlier: 4.116A pdb=" N THR F 115 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.873A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'F' and resid 403 through 439 removed outlier: 3.518A pdb=" N ALA F 417 " --> pdb=" O LEU F 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 81 No H-bonds generated for 'chain 'G' and resid 79 through 81' Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 363 through 402 Proline residue: G 399 - end of helix Processing helix chain 'G' and resid 410 through 417 Processing helix chain 'H' and resid 37 through 41 Processing helix chain 'H' and resid 46 through 51 removed outlier: 4.501A pdb=" N ALA H 50 " --> pdb=" O THR H 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'I' and resid 155 through 157 No H-bonds generated for 'chain 'I' and resid 155 through 157' Processing helix chain 'I' and resid 166 through 171 removed outlier: 3.559A pdb=" N LYS I 169 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER I 170 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 116 removed outlier: 3.921A pdb=" N THR J 115 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 254 Processing helix chain 'J' and resid 403 through 438 removed outlier: 3.757A pdb=" N ALA J 417 " --> pdb=" O LEU J 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 363 through 402 Proline residue: K 399 - end of helix Processing helix chain 'K' and resid 409 through 418 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 44 through 48 removed outlier: 3.667A pdb=" N LEU L 48 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 60 Processing helix chain 'M' and resid 143 through 149 Processing helix chain 'M' and resid 165 through 170 removed outlier: 4.257A pdb=" N SER M 170 " --> pdb=" O GLN M 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 116 removed outlier: 3.804A pdb=" N THR N 115 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 246 Processing helix chain 'N' and resid 250 through 254 Processing helix chain 'N' and resid 255 through 259 removed outlier: 3.915A pdb=" N GLY N 258 " --> pdb=" O ALA N 255 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS N 259 " --> pdb=" O PRO N 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 255 through 259' Processing helix chain 'N' and resid 403 through 438 removed outlier: 4.412A pdb=" N ALA N 417 " --> pdb=" O LEU N 413 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER N 418 " --> pdb=" O PHE N 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 224 No H-bonds generated for 'chain 'O' and resid 222 through 224' Processing helix chain 'O' and resid 351 through 363 removed outlier: 3.915A pdb=" N ILE O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 402 Proline residue: O 399 - end of helix removed outlier: 4.001A pdb=" N LEU O 402 " --> pdb=" O THR O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 418 removed outlier: 3.782A pdb=" N ILE O 418 " --> pdb=" O VAL O 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 42 Processing helix chain 'P' and resid 46 through 51 removed outlier: 4.527A pdb=" N ALA P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG P 60 " --> pdb=" O PRO P 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 60' Processing helix chain 'Q' and resid 37 through 41 Processing helix chain 'Q' and resid 44 through 48 Processing helix chain 'R' and resid 143 through 148 removed outlier: 3.797A pdb=" N ALA R 148 " --> pdb=" O GLU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 157 No H-bonds generated for 'chain 'R' and resid 155 through 157' Processing helix chain 'R' and resid 165 through 170 removed outlier: 4.159A pdb=" N SER R 170 " --> pdb=" O GLN R 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.750A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 5.316A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.714A pdb=" N LEU A 129 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.869A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.567A pdb=" N VAL A 108 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP A 75 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 306 removed outlier: 5.533A pdb=" N SER A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.546A pdb=" N CYS A 328 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.572A pdb=" N LEU B 285 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE B 319 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 287 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ARG B 317 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA B 289 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 315 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG B 291 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY B 313 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.908A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N ILE B 45 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N GLN B 104 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N VAL B 47 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU B 102 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA B 49 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE B 100 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 67 Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.942A pdb=" N ASP B 109 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 155 Processing sheet with id=AB8, first strand: chain 'B' and resid 237 through 238 removed outlier: 3.731A pdb=" N GLY B 164 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.514A pdb=" N PHE E 112 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR E 123 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE E 114 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR E 123 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 248 through 251 removed outlier: 4.913A pdb=" N PHE E 198 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ALA E 190 " --> pdb=" O PRO E 201 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 223 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 248 through 251 removed outlier: 6.312A pdb=" N VAL E 240 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 225 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TRP E 242 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA E 223 " --> pdb=" O TRP E 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 2 through 8 removed outlier: 4.422A pdb=" N LYS F 160 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 14 through 19 removed outlier: 5.269A pdb=" N ILE F 31 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 14 through 19 Processing sheet with id=AC8, first strand: chain 'F' and resid 42 through 48 removed outlier: 6.745A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 119 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.742A pdb=" N GLN F 59 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 51 through 54 removed outlier: 5.472A pdb=" N VAL F 108 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP F 75 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AD3, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'F' and resid 296 through 303 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 7.028A pdb=" N CYS F 306 " --> pdb=" O LYS F 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD7, first strand: chain 'F' and resid 387 through 388 removed outlier: 7.457A pdb=" N LEU G 285 " --> pdb=" O PHE G 319 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE G 319 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU G 287 " --> pdb=" O ARG G 317 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG G 317 " --> pdb=" O LEU G 287 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA G 289 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR G 315 " --> pdb=" O ALA G 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG G 291 " --> pdb=" O GLY G 313 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLY G 313 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 14 through 16 Processing sheet with id=AD9, first strand: chain 'G' and resid 31 through 35 removed outlier: 6.837A pdb=" N GLN G 46 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL G 34 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG G 44 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 12.276A pdb=" N SER G 48 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N PHE G 64 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 12.174A pdb=" N GLN G 50 " --> pdb=" O THR G 62 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N THR G 62 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY G 52 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 31 through 35 removed outlier: 6.837A pdb=" N GLN G 46 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL G 34 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG G 44 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N ILE G 45 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N GLN G 104 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N VAL G 47 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N LEU G 102 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ALA G 49 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE G 100 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR G 53 " --> pdb=" O HIS G 96 " (cutoff:3.500A) removed outlier: 12.380A pdb=" N HIS G 96 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 83 through 86 removed outlier: 3.715A pdb=" N SER G 110 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS G 128 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR G 112 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL G 126 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER G 114 " --> pdb=" O CYS G 124 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 148 through 155 Processing sheet with id=AE4, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AE5, first strand: chain 'G' and resid 180 through 183 Processing sheet with id=AE6, first strand: chain 'G' and resid 206 through 211 Processing sheet with id=AE7, first strand: chain 'H' and resid 20 through 25 removed outlier: 6.582A pdb=" N LEU H 20 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU H 111 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR H 22 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU H 113 " --> pdb=" O TYR H 22 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL H 24 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 54 " --> pdb=" O PHE H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.884A pdb=" N LEU H 73 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 72 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 140 through 141 removed outlier: 5.934A pdb=" N PHE I 112 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR I 123 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE I 114 " --> pdb=" O ASN I 121 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N TYR I 123 " --> pdb=" O PRO I 134 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 249 through 251 removed outlier: 4.849A pdb=" N PHE I 198 " --> pdb=" O LEU I 237 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ALA I 190 " --> pdb=" O PRO I 201 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA I 223 " --> pdb=" O ILE I 214 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 249 through 251 removed outlier: 6.837A pdb=" N VAL I 240 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL I 225 " --> pdb=" O VAL I 240 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 2 through 8 removed outlier: 4.180A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 14 through 19 removed outlier: 5.204A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU J 129 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 14 through 19 Processing sheet with id=AF6, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.223A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.919A pdb=" N GLN J 59 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 51 through 54 removed outlier: 5.518A pdb=" N VAL J 108 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP J 75 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AG1, first strand: chain 'J' and resid 219 through 221 Processing sheet with id=AG2, first strand: chain 'J' and resid 298 through 306 removed outlier: 3.596A pdb=" N GLU J 298 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 330 through 332 Processing sheet with id=AG4, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.953A pdb=" N ARG K 291 " --> pdb=" O GLY K 313 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY K 313 " --> pdb=" O ARG K 291 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 18 through 19 removed outlier: 3.992A pdb=" N TYR K 18 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N CYS K 124 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER K 114 " --> pdb=" O CYS K 124 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL K 126 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR K 112 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS K 128 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER K 110 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 31 through 35 removed outlier: 5.588A pdb=" N GLN K 46 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL K 34 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG K 44 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N SER K 48 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET K 67 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY K 52 " --> pdb=" O LYS K 63 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LYS K 63 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 31 through 35 removed outlier: 5.588A pdb=" N GLN K 46 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL K 34 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG K 44 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR K 99 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ALA K 49 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS K 97 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N PHE K 51 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N GLY K 95 " --> pdb=" O PHE K 51 " (cutoff:3.500A) removed outlier: 15.668A pdb=" N TYR K 53 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 17.667A pdb=" N ARG K 93 " --> pdb=" O TYR K 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 149 through 155 Processing sheet with id=AG9, first strand: chain 'K' and resid 237 through 238 removed outlier: 3.561A pdb=" N LEU K 255 " --> pdb=" O ILE K 166 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 180 through 183 Processing sheet with id=AH2, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AH3, first strand: chain 'K' and resid 206 through 207 removed outlier: 3.507A pdb=" N GLU K 200 " --> pdb=" O ILE K 227 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 275 through 279 removed outlier: 3.576A pdb=" N THR K 275 " --> pdb=" O HIS K 286 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG K 317 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 20 through 25 removed outlier: 6.319A pdb=" N LEU L 20 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU L 111 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR L 22 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU L 113 " --> pdb=" O TYR L 22 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL L 24 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN L 54 " --> pdb=" O PHE L 98 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 33 through 36 removed outlier: 6.552A pdb=" N PHE L 33 " --> pdb=" O VAL L 75 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL L 75 " --> pdb=" O PHE L 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY L 35 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR L 74 " --> pdb=" O ASP L 65 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP L 65 " --> pdb=" O TYR L 74 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 111 through 116 removed outlier: 6.337A pdb=" N LEU M 116 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL M 120 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR M 123 " --> pdb=" O PRO M 134 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 182 through 186 removed outlier: 9.144A pdb=" N ALA M 190 " --> pdb=" O PRO M 201 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE M 198 " --> pdb=" O LEU M 237 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL M 240 " --> pdb=" O VAL M 225 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL M 225 " --> pdb=" O VAL M 240 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP M 242 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA M 223 " --> pdb=" O TRP M 242 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 213 through 215 removed outlier: 3.931A pdb=" N ALA M 223 " --> pdb=" O ILE M 214 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA M 223 " --> pdb=" O TRP M 242 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP M 242 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL M 225 " --> pdb=" O VAL M 240 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL M 240 " --> pdb=" O VAL M 225 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 2 through 8 removed outlier: 4.072A pdb=" N LYS N 160 " --> pdb=" O ASP N 281 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 15 through 19 removed outlier: 4.988A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 140 through 147 removed outlier: 6.794A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 51 through 54 removed outlier: 3.732A pdb=" N GLN N 59 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 51 through 54 Processing sheet with id=AI6, first strand: chain 'N' and resid 203 through 204 Processing sheet with id=AI7, first strand: chain 'N' and resid 219 through 221 Processing sheet with id=AI8, first strand: chain 'N' and resid 296 through 303 removed outlier: 3.611A pdb=" N GLU N 298 " --> pdb=" O LYS N 321 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 330 through 332 Processing sheet with id=AJ1, first strand: chain 'N' and resid 387 through 388 Processing sheet with id=AJ2, first strand: chain 'N' and resid 387 through 388 removed outlier: 7.269A pdb=" N LEU O 285 " --> pdb=" O PHE O 319 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE O 319 " --> pdb=" O LEU O 285 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU O 287 " --> pdb=" O ARG O 317 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ARG O 317 " --> pdb=" O LEU O 287 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA O 289 " --> pdb=" O THR O 315 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR O 315 " --> pdb=" O ALA O 289 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG O 291 " --> pdb=" O GLY O 313 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY O 313 " --> pdb=" O ARG O 291 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 14 through 16 Processing sheet with id=AJ4, first strand: chain 'O' and resid 18 through 19 removed outlier: 4.368A pdb=" N TYR O 18 " --> pdb=" O THR O 125 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER O 117 " --> pdb=" O SER O 120 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP O 109 " --> pdb=" O LYS O 128 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 31 through 35 removed outlier: 6.930A pdb=" N GLN O 46 " --> pdb=" O GLU O 32 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL O 34 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG O 44 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR O 99 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ALA O 49 " --> pdb=" O LYS O 97 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LYS O 97 " --> pdb=" O ALA O 49 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N PHE O 51 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N GLY O 95 " --> pdb=" O PHE O 51 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 63 through 67 Processing sheet with id=AJ7, first strand: chain 'O' and resid 147 through 155 Processing sheet with id=AJ8, first strand: chain 'O' and resid 237 through 238 removed outlier: 3.836A pdb=" N ILE O 166 " --> pdb=" O LEU O 255 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 180 through 183 removed outlier: 4.574A pdb=" N VAL O 187 " --> pdb=" O MET O 217 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'O' and resid 206 through 211 Processing sheet with id=AK2, first strand: chain 'P' and resid 20 through 25 removed outlier: 6.529A pdb=" N LEU P 20 " --> pdb=" O GLU P 109 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU P 111 " --> pdb=" O LEU P 20 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR P 22 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU P 113 " --> pdb=" O TYR P 22 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL P 24 " --> pdb=" O LEU P 113 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN P 54 " --> pdb=" O PHE P 98 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P' and resid 33 through 36 removed outlier: 7.150A pdb=" N LEU P 73 " --> pdb=" O VAL P 34 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Q' and resid 20 through 24 removed outlier: 3.536A pdb=" N GLN Q 54 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Q' and resid 33 through 36 removed outlier: 6.521A pdb=" N PHE Q 33 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL Q 75 " --> pdb=" O PHE Q 33 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'R' and resid 140 through 141 removed outlier: 3.901A pdb=" N GLY R 122 " --> pdb=" O ILE R 114 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU R 116 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR R 123 " --> pdb=" O PRO R 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU R 159 " --> pdb=" O ALA R 154 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'R' and resid 249 through 251 removed outlier: 4.892A pdb=" N PHE R 198 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N ALA R 190 " --> pdb=" O PRO R 201 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA R 223 " --> pdb=" O ILE R 214 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'R' and resid 249 through 251 removed outlier: 6.491A pdb=" N VAL R 240 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL R 225 " --> pdb=" O VAL R 240 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3426 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: 19.95 Time building geometry restraints manager: 9.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10101 1.33 - 1.46: 7706 1.46 - 1.58: 16749 1.58 - 1.71: 0 1.71 - 1.83: 244 Bond restraints: 34800 Sorted by residual: bond pdb=" N TYR F 85 " pdb=" CA TYR F 85 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.10e-03 1.98e+04 1.69e+01 bond pdb=" N VAL R 239 " pdb=" CA VAL R 239 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.03e+01 bond pdb=" N VAL N 177 " pdb=" CA VAL N 177 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N ASP G 70 " pdb=" CA ASP G 70 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N VAL P 24 " pdb=" CA VAL P 24 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.85e+00 ... (remaining 34795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 43888 1.66 - 3.32: 3056 3.32 - 4.98: 369 4.98 - 6.64: 51 6.64 - 8.30: 16 Bond angle restraints: 47380 Sorted by residual: angle pdb=" N ASP G 72 " pdb=" CA ASP G 72 " pdb=" C ASP G 72 " ideal model delta sigma weight residual 113.28 106.18 7.10 1.22e+00 6.72e-01 3.39e+01 angle pdb=" CB HIS F 230 " pdb=" CG HIS F 230 " pdb=" CD2 HIS F 230 " ideal model delta sigma weight residual 131.20 124.56 6.64 1.30e+00 5.92e-01 2.61e+01 angle pdb=" CB HIS L 94 " pdb=" CG HIS L 94 " pdb=" CD2 HIS L 94 " ideal model delta sigma weight residual 131.20 125.14 6.06 1.30e+00 5.92e-01 2.17e+01 angle pdb=" C GLN G 50 " pdb=" N PHE G 51 " pdb=" CA PHE G 51 " ideal model delta sigma weight residual 121.39 129.01 -7.62 1.66e+00 3.63e-01 2.11e+01 angle pdb=" OE1 GLN L 19 " pdb=" CD GLN L 19 " pdb=" NE2 GLN L 19 " ideal model delta sigma weight residual 122.60 118.34 4.26 1.00e+00 1.00e+00 1.82e+01 ... (remaining 47375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18728 17.92 - 35.84: 1675 35.84 - 53.76: 348 53.76 - 71.68: 113 71.68 - 89.60: 28 Dihedral angle restraints: 20892 sinusoidal: 8196 harmonic: 12696 Sorted by residual: dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -145.11 59.11 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CA ARG Q 81 " pdb=" C ARG Q 81 " pdb=" N GLU Q 82 " pdb=" CA GLU Q 82 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA THR G 234 " pdb=" C THR G 234 " pdb=" N LYS G 235 " pdb=" CA LYS G 235 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 20889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4046 0.057 - 0.115: 1077 0.115 - 0.172: 192 0.172 - 0.230: 22 0.230 - 0.287: 3 Chirality restraints: 5340 Sorted by residual: chirality pdb=" CA SER G 22 " pdb=" N SER G 22 " pdb=" C SER G 22 " pdb=" CB SER G 22 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA PRO G 241 " pdb=" N PRO G 241 " pdb=" C PRO G 241 " pdb=" CB PRO G 241 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB THR G 125 " pdb=" CA THR G 125 " pdb=" OG1 THR G 125 " pdb=" CG2 THR G 125 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 5337 not shown) Planarity restraints: 6104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 99 " -0.112 2.00e-02 2.50e+03 5.65e-02 6.39e+01 pdb=" CG TYR G 99 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR G 99 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR G 99 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR G 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR G 99 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR G 99 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR G 99 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 176 " -0.085 2.00e-02 2.50e+03 4.46e-02 3.98e+01 pdb=" CG TYR G 176 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR G 176 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR G 176 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR G 176 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR G 176 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR G 176 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR G 176 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 230 " -0.055 2.00e-02 2.50e+03 4.13e-02 2.56e+01 pdb=" CG HIS F 230 " 0.067 2.00e-02 2.50e+03 pdb=" ND1 HIS F 230 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS F 230 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS F 230 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS F 230 " -0.032 2.00e-02 2.50e+03 ... (remaining 6101 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3589 2.74 - 3.28: 33818 3.28 - 3.82: 56096 3.82 - 4.36: 64070 4.36 - 4.90: 111169 Nonbonded interactions: 268742 Sorted by model distance: nonbonded pdb=" OG1 THR G 297 " pdb=" OG1 THR G 307 " model vdw 2.200 3.040 nonbonded pdb=" OE1 GLU G 186 " pdb=" OH TYR G 188 " model vdw 2.205 3.040 nonbonded pdb=" O GLU N 292 " pdb=" NH1 ARG N 324 " model vdw 2.210 3.120 nonbonded pdb=" O PRO R 180 " pdb=" OH TYR R 184 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR Q 22 " pdb=" OD2 ASP Q 40 " model vdw 2.215 3.040 ... (remaining 268737 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } 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: 1.780 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: 0.040 Extract box with map and model: 1.340 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 85.170 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.420 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: 0.030 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.008 0.102 34852 Z= 0.397 Angle : 0.903 8.295 47484 Z= 0.537 Chirality : 0.053 0.287 5340 Planarity : 0.010 0.126 6104 Dihedral : 14.953 89.599 12600 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 1.20 % Allowed : 13.56 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.57 (0.13), residues: 4368 helix: 1.22 (0.24), residues: 502 sheet: -0.29 (0.14), residues: 1384 loop : -0.72 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP G 35 HIS 0.012 0.002 HIS G 21 PHE 0.056 0.003 PHE G 51 TYR 0.112 0.006 TYR G 99 ARG 0.029 0.004 ARG J 21 Details of bonding type rmsd hydrogen bonds : bond 0.21286 ( 1213) hydrogen bonds : angle 7.83154 ( 3426) SS BOND : bond 0.00522 ( 52) SS BOND : angle 1.45542 ( 104) covalent geometry : bond 0.00758 (34800) covalent geometry : angle 0.90187 (47380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 1354 time to evaluate : 4.056 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: 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: 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: 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 88 MET cc_start: 0.8565 (mtp) cc_final: 0.8124 (mtp) REVERT: A 93 GLN cc_start: 0.8651 (mm110) cc_final: 0.8144 (mm110) REVERT: A 98 SER cc_start: 0.9155 (t) cc_final: 0.8256 (p) REVERT: A 171 SER cc_start: 0.9217 (m) cc_final: 0.8905 (p) REVERT: A 204 GLN cc_start: 0.8451 (mt0) cc_final: 0.8053 (mt0) REVERT: A 207 SER cc_start: 0.8908 (m) cc_final: 0.8489 (p) REVERT: A 212 ASP cc_start: 0.9017 (p0) cc_final: 0.8711 (p0) REVERT: A 218 ASP cc_start: 0.8498 (t0) cc_final: 0.8171 (t0) REVERT: A 238 SER cc_start: 0.9284 (t) cc_final: 0.8288 (p) REVERT: A 242 MET cc_start: 0.9453 (mmm) cc_final: 0.8786 (mmm) REVERT: A 260 LYS cc_start: 0.8669 (tttm) cc_final: 0.8066 (tttm) REVERT: A 261 ILE cc_start: 0.9377 (mm) cc_final: 0.9046 (tp) REVERT: A 271 CYS cc_start: 0.8956 (t) cc_final: 0.8536 (m) REVERT: A 293 SER cc_start: 0.9308 (t) cc_final: 0.9018 (p) REVERT: A 340 LYS cc_start: 0.9290 (tttt) cc_final: 0.9046 (ttpp) REVERT: A 341 GLU cc_start: 0.8437 (mp0) cc_final: 0.7507 (mp0) REVERT: A 394 VAL cc_start: 0.9100 (t) cc_final: 0.8825 (p) REVERT: A 399 GLN cc_start: 0.8736 (tp40) cc_final: 0.8396 (mp10) REVERT: A 403 SER cc_start: 0.9307 (p) cc_final: 0.9097 (p) REVERT: A 433 MET cc_start: 0.7630 (mmp) cc_final: 0.7282 (tpt) REVERT: B 80 MET cc_start: 0.7302 (mmt) cc_final: 0.6095 (mmt) REVERT: B 104 GLN cc_start: 0.8104 (tt0) cc_final: 0.7847 (tm-30) REVERT: B 142 PHE cc_start: 0.8355 (m-80) cc_final: 0.8104 (m-80) REVERT: B 156 ASP cc_start: 0.8522 (t0) cc_final: 0.8007 (t70) REVERT: B 168 MET cc_start: 0.8553 (ptp) cc_final: 0.8317 (mtp) REVERT: B 305 ASP cc_start: 0.9046 (m-30) cc_final: 0.8703 (m-30) REVERT: B 330 TRP cc_start: 0.9356 (t-100) cc_final: 0.8707 (t-100) REVERT: B 342 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 347 ASP cc_start: 0.8558 (t70) cc_final: 0.8324 (t70) REVERT: B 393 ARG cc_start: 0.7935 (tmm160) cc_final: 0.7731 (ttp80) REVERT: B 394 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7706 (mtt90) REVERT: E 156 MET cc_start: 0.8548 (ppp) cc_final: 0.7880 (ppp) REVERT: E 216 ASP cc_start: 0.8287 (t0) cc_final: 0.7853 (t70) REVERT: E 250 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8442 (ttpp) REVERT: F 195 MET cc_start: 0.8884 (mpp) cc_final: 0.8497 (mpp) REVERT: F 218 ASP cc_start: 0.8756 (t0) cc_final: 0.8090 (t0) REVERT: F 262 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7741 (mp0) REVERT: F 305 ASP cc_start: 0.9330 (t0) cc_final: 0.9116 (t0) REVERT: F 311 ASP cc_start: 0.7815 (p0) cc_final: 0.7585 (p0) REVERT: F 320 TYR cc_start: 0.8050 (p90) cc_final: 0.7579 (p90) REVERT: F 339 LEU cc_start: 0.9313 (mp) cc_final: 0.8991 (mp) REVERT: F 341 GLU cc_start: 0.7569 (mp0) cc_final: 0.7180 (mp0) REVERT: F 367 VAL cc_start: 0.8952 (t) cc_final: 0.8139 (m) REVERT: F 374 THR cc_start: 0.7944 (m) cc_final: 0.7164 (p) REVERT: F 394 VAL cc_start: 0.9036 (t) cc_final: 0.8597 (p) REVERT: F 433 MET cc_start: 0.7411 (mmt) cc_final: 0.6910 (tpp) REVERT: G 21 HIS cc_start: 0.8787 (m90) cc_final: 0.8545 (m-70) REVERT: G 67 MET cc_start: 0.8550 (tpp) cc_final: 0.8316 (tpt) REVERT: G 76 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8716 (mmtp) REVERT: G 125 THR cc_start: 0.9073 (m) cc_final: 0.8705 (p) REVERT: G 191 PRO cc_start: 0.8430 (Cg_exo) cc_final: 0.8178 (Cg_endo) REVERT: G 347 ASP cc_start: 0.8071 (t0) cc_final: 0.7849 (t0) REVERT: G 360 TYR cc_start: 0.8770 (t80) cc_final: 0.8206 (t80) REVERT: G 393 ARG cc_start: 0.7622 (ttt90) cc_final: 0.7346 (tpp80) REVERT: H 20 LEU cc_start: 0.8417 (mt) cc_final: 0.7727 (tt) REVERT: H 36 ASN cc_start: 0.6731 (t0) cc_final: 0.6396 (t0) REVERT: I 130 ARG cc_start: 0.8607 (ptp-110) cc_final: 0.8352 (ptt-90) REVERT: I 193 TYR cc_start: 0.8210 (t80) cc_final: 0.7648 (t80) REVERT: I 222 VAL cc_start: 0.8968 (t) cc_final: 0.8628 (m) REVERT: I 243 ASN cc_start: 0.8530 (t0) cc_final: 0.8187 (m-40) REVERT: I 249 ILE cc_start: 0.7720 (mt) cc_final: 0.7364 (mt) REVERT: J 2 GLU cc_start: 0.8887 (tt0) cc_final: 0.8667 (tp30) REVERT: J 3 HIS cc_start: 0.7424 (t70) cc_final: 0.6789 (t-170) REVERT: J 13 ILE cc_start: 0.9171 (mm) cc_final: 0.8931 (tp) REVERT: J 15 TYR cc_start: 0.8766 (t80) cc_final: 0.8228 (t80) REVERT: J 20 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8449 (pm20) REVERT: J 31 ILE cc_start: 0.8867 (mt) cc_final: 0.8244 (mt) REVERT: J 37 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8472 (mm-30) REVERT: J 43 ASN cc_start: 0.8735 (p0) cc_final: 0.8308 (p0) REVERT: J 45 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8763 (mm-30) REVERT: J 66 LEU cc_start: 0.8017 (mt) cc_final: 0.7728 (mp) REVERT: J 75 ASP cc_start: 0.8461 (t0) cc_final: 0.8001 (t0) REVERT: J 101 THR cc_start: 0.8188 (m) cc_final: 0.7765 (m) REVERT: J 174 ASP cc_start: 0.8564 (m-30) cc_final: 0.8190 (m-30) REVERT: J 251 LEU cc_start: 0.8947 (tp) cc_final: 0.8589 (tp) REVERT: J 257 PHE cc_start: 0.9121 (m-80) cc_final: 0.8883 (m-10) REVERT: J 262 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8115 (mm-30) REVERT: J 279 SER cc_start: 0.9122 (t) cc_final: 0.8637 (m) REVERT: J 280 ILE cc_start: 0.8245 (mp) cc_final: 0.7882 (mm) REVERT: J 292 GLU cc_start: 0.9454 (tp30) cc_final: 0.9204 (mp0) REVERT: J 366 ILE cc_start: 0.9199 (mt) cc_final: 0.8668 (tp) REVERT: J 373 LYS cc_start: 0.9285 (mttm) cc_final: 0.8881 (mttm) REVERT: J 407 TRP cc_start: 0.8067 (m100) cc_final: 0.7753 (m100) REVERT: J 409 TRP cc_start: 0.7686 (m100) cc_final: 0.7479 (m100) REVERT: K 78 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7329 (t0) REVERT: K 96 HIS cc_start: 0.7611 (p90) cc_final: 0.7192 (p90) REVERT: K 141 LEU cc_start: 0.9548 (tp) cc_final: 0.8961 (tt) REVERT: K 156 ASP cc_start: 0.8803 (t0) cc_final: 0.7949 (t0) REVERT: K 158 LEU cc_start: 0.8795 (mt) cc_final: 0.8269 (mt) REVERT: K 225 GLN cc_start: 0.8587 (mt0) cc_final: 0.8161 (mt0) REVERT: K 235 LYS cc_start: 0.6696 (tmtp) cc_final: 0.5873 (mmmt) REVERT: K 360 TYR cc_start: 0.8951 (t80) cc_final: 0.8637 (t80) REVERT: L 56 VAL cc_start: 0.9366 (t) cc_final: 0.8668 (m) REVERT: L 58 ASN cc_start: 0.8666 (p0) cc_final: 0.8458 (t0) REVERT: L 92 VAL cc_start: 0.8449 (t) cc_final: 0.7902 (t) REVERT: L 105 LEU cc_start: 0.9086 (tp) cc_final: 0.8054 (tp) REVERT: L 106 PHE cc_start: 0.7815 (m-80) cc_final: 0.7027 (m-80) REVERT: L 109 GLU cc_start: 0.8601 (tt0) cc_final: 0.8096 (pm20) REVERT: L 111 GLU cc_start: 0.8643 (tt0) cc_final: 0.8314 (tp30) REVERT: L 113 LEU cc_start: 0.8572 (mt) cc_final: 0.8265 (mp) REVERT: M 110 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7524 (mtpp) REVERT: M 125 CYS cc_start: 0.7742 (t) cc_final: 0.7421 (t) REVERT: M 176 THR cc_start: 0.7985 (t) cc_final: 0.6761 (m) REVERT: M 183 PHE cc_start: 0.7992 (m-80) cc_final: 0.7684 (m-10) REVERT: N 15 TYR cc_start: 0.8869 (t80) cc_final: 0.8393 (t80) REVERT: N 31 ILE cc_start: 0.8755 (mt) cc_final: 0.8039 (mt) REVERT: N 75 ASP cc_start: 0.8881 (t0) cc_final: 0.8507 (t0) REVERT: N 88 MET cc_start: 0.7976 (mmt) cc_final: 0.6769 (mmt) REVERT: N 93 GLN cc_start: 0.8798 (tp40) cc_final: 0.8267 (tp40) REVERT: N 117 ASP cc_start: 0.8957 (t0) cc_final: 0.8629 (t0) REVERT: N 125 HIS cc_start: 0.7754 (m90) cc_final: 0.7093 (m90) REVERT: N 162 ILE cc_start: 0.9122 (mp) cc_final: 0.8691 (tp) REVERT: N 213 ILE cc_start: 0.8878 (mt) cc_final: 0.8571 (mp) REVERT: N 218 ASP cc_start: 0.8721 (t70) cc_final: 0.8488 (t0) REVERT: N 264 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8650 (tm-30) REVERT: N 298 GLU cc_start: 0.8635 (pm20) cc_final: 0.8405 (pm20) REVERT: N 331 HIS cc_start: 0.8519 (t-170) cc_final: 0.7769 (t70) REVERT: N 366 ILE cc_start: 0.9297 (mt) cc_final: 0.9070 (tp) REVERT: N 379 GLU cc_start: 0.8046 (tp30) cc_final: 0.7835 (tp30) REVERT: N 387 ILE cc_start: 0.9169 (mm) cc_final: 0.8827 (mm) REVERT: N 396 GLN cc_start: 0.9332 (tt0) cc_final: 0.8752 (tt0) REVERT: N 399 GLN cc_start: 0.7582 (mp10) cc_final: 0.7372 (mp10) REVERT: N 411 LEU cc_start: 0.8844 (mt) cc_final: 0.8554 (tt) REVERT: O 34 VAL cc_start: 0.9577 (t) cc_final: 0.9305 (m) REVERT: O 36 ASP cc_start: 0.9164 (p0) cc_final: 0.8942 (p0) REVERT: O 67 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7987 (tpp) REVERT: O 80 MET cc_start: 0.9336 (mmp) cc_final: 0.8918 (mmt) REVERT: O 127 GLU cc_start: 0.5784 (mm-30) cc_final: 0.5531 (tm-30) REVERT: O 138 GLU cc_start: 0.8658 (tt0) cc_final: 0.8065 (tt0) REVERT: O 165 TYR cc_start: 0.9007 (p90) cc_final: 0.8539 (p90) REVERT: O 168 MET cc_start: 0.8179 (mmm) cc_final: 0.7717 (tpp) REVERT: O 225 GLN cc_start: 0.7572 (mt0) cc_final: 0.7311 (mt0) REVERT: O 238 PHE cc_start: 0.8921 (t80) cc_final: 0.8704 (t80) REVERT: O 239 ASN cc_start: 0.9146 (t0) cc_final: 0.8921 (t0) REVERT: O 334 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8912 (mm-30) REVERT: O 351 TRP cc_start: 0.8427 (m100) cc_final: 0.7720 (m-90) REVERT: P 80 ASP cc_start: 0.8205 (t0) cc_final: 0.7473 (m-30) REVERT: P 95 LEU cc_start: 0.8187 (tp) cc_final: 0.7956 (tp) REVERT: P 96 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8129 (mp0) REVERT: P 101 ASN cc_start: 0.8746 (m-40) cc_final: 0.7921 (p0) REVERT: Q 26 GLU cc_start: 0.6458 (pt0) cc_final: 0.6151 (pt0) REVERT: Q 55 THR cc_start: 0.8759 (p) cc_final: 0.8555 (t) REVERT: Q 103 LEU cc_start: 0.8776 (mt) cc_final: 0.8367 (mt) REVERT: R 125 CYS cc_start: 0.8463 (t) cc_final: 0.7400 (t) REVERT: R 127 VAL cc_start: 0.8976 (t) cc_final: 0.8473 (m) REVERT: R 130 ARG cc_start: 0.8246 (ptp-110) cc_final: 0.7982 (ptp-170) REVERT: R 132 MET cc_start: 0.8710 (mpp) cc_final: 0.8261 (mpp) REVERT: R 193 TYR cc_start: 0.8680 (t80) cc_final: 0.8336 (t80) REVERT: R 209 ASP cc_start: 0.7778 (m-30) cc_final: 0.7354 (t0) REVERT: R 212 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7875 (mtt-85) outliers start: 45 outliers final: 9 residues processed: 1375 average time/residue: 0.5324 time to fit residues: 1184.9297 Evaluate side-chains 898 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 887 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 131 optimal weight: 40.0000 chunk 205 optimal weight: 40.0000 chunk 252 optimal weight: 0.8980 chunk 392 optimal weight: 4.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 59 GLN A 396 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 233 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN E 192 GLN ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN G 252 GLN ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 HIS H 28 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 235 GLN J 327 HIS ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 HIS ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 GLN L 19 GLN L 94 HIS M 119 GLN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN ** N 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS N 331 HIS N 396 GLN ** O 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 GLN R 143 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110868 restraints weight = 75956.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114152 restraints weight = 38890.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116344 restraints weight = 25018.691| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34852 Z= 0.204 Angle : 0.676 11.552 47484 Z= 0.358 Chirality : 0.047 0.227 5340 Planarity : 0.005 0.057 6104 Dihedral : 5.176 25.811 4744 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.27 % Allowed : 3.98 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.38 (0.13), residues: 4368 helix: 1.65 (0.24), residues: 510 sheet: -0.21 (0.14), residues: 1359 loop : -0.64 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 186 HIS 0.015 0.001 HIS B 174 PHE 0.030 0.002 PHE L 106 TYR 0.034 0.002 TYR K 206 ARG 0.011 0.001 ARG F 134 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 1213) hydrogen bonds : angle 5.96828 ( 3426) SS BOND : bond 0.00537 ( 52) SS BOND : angle 1.86592 ( 104) covalent geometry : bond 0.00461 (34800) covalent geometry : angle 0.67138 (47380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1078 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8571 (mtp) cc_final: 0.8291 (mtp) REVERT: A 212 ASP cc_start: 0.8776 (p0) cc_final: 0.8437 (p0) REVERT: A 240 TYR cc_start: 0.9247 (t80) cc_final: 0.8917 (t80) REVERT: A 341 GLU cc_start: 0.8617 (mp0) cc_final: 0.8283 (mp0) REVERT: A 403 SER cc_start: 0.8863 (p) cc_final: 0.8642 (p) REVERT: A 433 MET cc_start: 0.7653 (mmp) cc_final: 0.7243 (tpp) REVERT: B 80 MET cc_start: 0.7341 (mmt) cc_final: 0.6447 (mmt) REVERT: B 121 GLU cc_start: 0.8520 (pm20) cc_final: 0.8121 (pm20) REVERT: B 156 ASP cc_start: 0.7680 (t0) cc_final: 0.7465 (t0) REVERT: E 125 CYS cc_start: 0.7123 (m) cc_final: 0.6547 (m) REVERT: E 186 TRP cc_start: 0.8070 (t60) cc_final: 0.7843 (t60) REVERT: E 194 GLU cc_start: 0.8357 (pp20) cc_final: 0.8059 (pp20) REVERT: E 197 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8175 (mtm110) REVERT: E 216 ASP cc_start: 0.8511 (t0) cc_final: 0.7940 (t70) REVERT: F 195 MET cc_start: 0.8922 (mpp) cc_final: 0.8328 (mpp) REVERT: F 218 ASP cc_start: 0.8468 (t0) cc_final: 0.8096 (t0) REVERT: F 246 ASN cc_start: 0.8790 (t0) cc_final: 0.8538 (t0) REVERT: F 262 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7690 (mp0) REVERT: F 280 ILE cc_start: 0.9212 (mm) cc_final: 0.9006 (mm) REVERT: F 320 TYR cc_start: 0.8096 (p90) cc_final: 0.7658 (p90) REVERT: F 340 LYS cc_start: 0.9428 (tttp) cc_final: 0.8980 (ttpp) REVERT: F 365 PHE cc_start: 0.8743 (p90) cc_final: 0.8394 (p90) REVERT: F 367 VAL cc_start: 0.9053 (t) cc_final: 0.8686 (m) REVERT: F 374 THR cc_start: 0.8228 (m) cc_final: 0.7879 (p) REVERT: F 394 VAL cc_start: 0.9288 (t) cc_final: 0.8974 (p) REVERT: F 433 MET cc_start: 0.7365 (mmt) cc_final: 0.7092 (tpp) REVERT: G 168 MET cc_start: 0.7612 (mtp) cc_final: 0.7354 (mtm) REVERT: G 347 ASP cc_start: 0.8024 (t0) cc_final: 0.7746 (t0) REVERT: G 360 TYR cc_start: 0.8899 (t80) cc_final: 0.8133 (t80) REVERT: G 367 THR cc_start: 0.8972 (m) cc_final: 0.8708 (p) REVERT: G 393 ARG cc_start: 0.7917 (ttt90) cc_final: 0.7553 (tpp80) REVERT: G 395 ASP cc_start: 0.8524 (m-30) cc_final: 0.8086 (m-30) REVERT: H 20 LEU cc_start: 0.8038 (mt) cc_final: 0.7200 (tt) REVERT: H 63 TYR cc_start: 0.7979 (m-80) cc_final: 0.7632 (m-80) REVERT: H 67 ASN cc_start: 0.8361 (t0) cc_final: 0.8085 (t0) REVERT: I 143 ASN cc_start: 0.8449 (t0) cc_final: 0.8226 (t0) REVERT: I 174 GLN cc_start: 0.8903 (mm110) cc_final: 0.8660 (mm110) REVERT: I 193 TYR cc_start: 0.8117 (t80) cc_final: 0.7749 (t80) REVERT: I 198 PHE cc_start: 0.8823 (m-10) cc_final: 0.8547 (m-10) REVERT: I 222 VAL cc_start: 0.8876 (t) cc_final: 0.8586 (m) REVERT: I 243 ASN cc_start: 0.8302 (t0) cc_final: 0.7839 (m-40) REVERT: J 3 HIS cc_start: 0.8280 (t70) cc_final: 0.7673 (t70) REVERT: J 57 SER cc_start: 0.9097 (m) cc_final: 0.7897 (p) REVERT: J 75 ASP cc_start: 0.8199 (t0) cc_final: 0.7769 (t0) REVERT: J 251 LEU cc_start: 0.9194 (tp) cc_final: 0.8829 (tp) REVERT: J 262 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8183 (mm-30) REVERT: J 278 ILE cc_start: 0.9546 (tt) cc_final: 0.9288 (mm) REVERT: J 366 ILE cc_start: 0.9342 (mt) cc_final: 0.9027 (tp) REVERT: J 390 GLU cc_start: 0.8470 (tt0) cc_final: 0.7453 (tm-30) REVERT: J 404 LYS cc_start: 0.8927 (mppt) cc_final: 0.8510 (tppt) REVERT: J 407 TRP cc_start: 0.8544 (m100) cc_final: 0.7927 (m100) REVERT: J 439 ARG cc_start: 0.6561 (ttp80) cc_final: 0.6352 (ptt180) REVERT: K 46 GLN cc_start: 0.7920 (tt0) cc_final: 0.7477 (tt0) REVERT: K 54 ASN cc_start: 0.7980 (p0) cc_final: 0.7767 (p0) REVERT: K 96 HIS cc_start: 0.7543 (p90) cc_final: 0.7009 (p90) REVERT: K 104 GLN cc_start: 0.8571 (tp40) cc_final: 0.8370 (tp-100) REVERT: K 141 LEU cc_start: 0.9355 (tp) cc_final: 0.9030 (tt) REVERT: K 156 ASP cc_start: 0.8395 (t0) cc_final: 0.8066 (t0) REVERT: K 225 GLN cc_start: 0.8276 (mt0) cc_final: 0.7842 (mt0) REVERT: K 235 LYS cc_start: 0.5425 (tttm) cc_final: 0.4858 (mmmt) REVERT: K 305 ASP cc_start: 0.8206 (t0) cc_final: 0.7961 (t0) REVERT: K 330 TRP cc_start: 0.9283 (t-100) cc_final: 0.8939 (t-100) REVERT: K 342 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8059 (mm-30) REVERT: K 360 TYR cc_start: 0.9062 (t80) cc_final: 0.8665 (t80) REVERT: L 20 LEU cc_start: 0.7384 (mt) cc_final: 0.7171 (mt) REVERT: L 26 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8404 (tm-30) REVERT: L 80 ASP cc_start: 0.8086 (t0) cc_final: 0.7582 (t0) REVERT: L 92 VAL cc_start: 0.8591 (t) cc_final: 0.8131 (t) REVERT: L 101 ASN cc_start: 0.8668 (t0) cc_final: 0.7673 (m-40) REVERT: L 104 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6533 (tm-30) REVERT: L 105 LEU cc_start: 0.8628 (tp) cc_final: 0.8355 (tp) REVERT: L 108 VAL cc_start: 0.9045 (t) cc_final: 0.8788 (m) REVERT: L 109 GLU cc_start: 0.8503 (tt0) cc_final: 0.8224 (pm20) REVERT: L 111 GLU cc_start: 0.8686 (tt0) cc_final: 0.8484 (tp30) REVERT: M 125 CYS cc_start: 0.7626 (t) cc_final: 0.7392 (t) REVERT: M 149 VAL cc_start: 0.8190 (t) cc_final: 0.7920 (p) REVERT: M 176 THR cc_start: 0.7888 (t) cc_final: 0.6542 (t) REVERT: M 178 ASP cc_start: 0.8046 (p0) cc_final: 0.7619 (p0) REVERT: M 183 PHE cc_start: 0.7999 (m-80) cc_final: 0.7651 (m-10) REVERT: M 194 GLU cc_start: 0.8719 (tt0) cc_final: 0.8506 (pp20) REVERT: M 195 ASN cc_start: 0.8782 (m-40) cc_final: 0.8271 (m-40) REVERT: M 220 ARG cc_start: 0.8775 (mtm180) cc_final: 0.8260 (mtm180) REVERT: N 15 TYR cc_start: 0.8960 (t80) cc_final: 0.8700 (t80) REVERT: N 93 GLN cc_start: 0.8679 (tp40) cc_final: 0.7881 (tp40) REVERT: N 143 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8142 (ttm-80) REVERT: N 144 LEU cc_start: 0.8760 (mt) cc_final: 0.8413 (mt) REVERT: N 187 TYR cc_start: 0.8924 (t80) cc_final: 0.8632 (t80) REVERT: N 264 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8323 (tm-30) REVERT: N 321 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8653 (mtmm) REVERT: N 396 GLN cc_start: 0.9208 (tt0) cc_final: 0.8778 (tt0) REVERT: O 34 VAL cc_start: 0.9615 (t) cc_final: 0.9295 (m) REVERT: O 36 ASP cc_start: 0.9006 (p0) cc_final: 0.8716 (p0) REVERT: O 67 MET cc_start: 0.8228 (tpp) cc_final: 0.7894 (tpp) REVERT: O 80 MET cc_start: 0.9148 (mmp) cc_final: 0.8244 (mmm) REVERT: O 125 THR cc_start: 0.9337 (m) cc_final: 0.8846 (p) REVERT: O 165 TYR cc_start: 0.8487 (p90) cc_final: 0.8201 (p90) REVERT: O 224 LYS cc_start: 0.9431 (pttm) cc_final: 0.9219 (pttp) REVERT: O 239 ASN cc_start: 0.9272 (t0) cc_final: 0.8955 (t0) REVERT: O 334 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8368 (mm-30) REVERT: P 61 THR cc_start: 0.8608 (p) cc_final: 0.8369 (p) REVERT: P 69 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8776 (mp0) REVERT: P 95 LEU cc_start: 0.7856 (tp) cc_final: 0.7528 (tp) REVERT: Q 55 THR cc_start: 0.8709 (p) cc_final: 0.8485 (t) REVERT: Q 99 LEU cc_start: 0.9036 (mt) cc_final: 0.8832 (mt) REVERT: Q 104 GLU cc_start: 0.6583 (mp0) cc_final: 0.6266 (mp0) REVERT: R 115 MET cc_start: 0.8694 (mmm) cc_final: 0.8367 (mmm) REVERT: R 116 LEU cc_start: 0.9150 (tp) cc_final: 0.8753 (tp) REVERT: R 125 CYS cc_start: 0.8893 (t) cc_final: 0.8215 (t) REVERT: R 126 VAL cc_start: 0.9531 (m) cc_final: 0.9302 (m) REVERT: R 127 VAL cc_start: 0.9166 (t) cc_final: 0.8842 (m) REVERT: R 133 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8371 (tttm) REVERT: R 143 ASN cc_start: 0.6011 (m-40) cc_final: 0.5559 (t0) REVERT: R 157 TYR cc_start: 0.7902 (m-80) cc_final: 0.7672 (m-10) REVERT: R 160 GLU cc_start: 0.8420 (mp0) cc_final: 0.7639 (mp0) REVERT: R 193 TYR cc_start: 0.8568 (t80) cc_final: 0.8358 (t80) REVERT: R 195 ASN cc_start: 0.8397 (p0) cc_final: 0.8000 (p0) REVERT: R 197 ARG cc_start: 0.9298 (ttm-80) cc_final: 0.9014 (ttm-80) REVERT: R 207 LYS cc_start: 0.9240 (tttm) cc_final: 0.8998 (tptp) REVERT: R 209 ASP cc_start: 0.8203 (m-30) cc_final: 0.7796 (t0) outliers start: 10 outliers final: 3 residues processed: 1086 average time/residue: 0.5041 time to fit residues: 897.5479 Evaluate side-chains 817 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 814 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 37 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 362 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 256 optimal weight: 8.9990 chunk 385 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN B 174 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS E 192 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 HIS ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 GLN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN N 204 GLN N 345 HIS O 50 GLN O 169 HIS P 19 GLN P 21 HIS ** R 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102041 restraints weight = 77740.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105984 restraints weight = 39696.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107449 restraints weight = 22091.050| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 34852 Z= 0.312 Angle : 0.738 10.898 47484 Z= 0.388 Chirality : 0.048 0.234 5340 Planarity : 0.005 0.057 6104 Dihedral : 5.366 25.237 4744 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.49 (0.13), residues: 4368 helix: 1.57 (0.23), residues: 506 sheet: -0.27 (0.14), residues: 1365 loop : -0.72 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 242 HIS 0.012 0.002 HIS O 73 PHE 0.027 0.002 PHE B 51 TYR 0.025 0.002 TYR J 107 ARG 0.030 0.001 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 1213) hydrogen bonds : angle 5.78203 ( 3426) SS BOND : bond 0.00512 ( 52) SS BOND : angle 1.61752 ( 104) covalent geometry : bond 0.00694 (34800) covalent geometry : angle 0.73511 (47380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 945 time to evaluate : 4.510 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8761 (p0) cc_final: 0.8357 (p0) REVERT: A 321 LYS cc_start: 0.9640 (mtpt) cc_final: 0.9412 (mtpp) REVERT: A 362 GLN cc_start: 0.8890 (pt0) cc_final: 0.8661 (pt0) REVERT: A 433 MET cc_start: 0.7746 (mmp) cc_final: 0.7360 (tpp) REVERT: B 80 MET cc_start: 0.7449 (mmt) cc_final: 0.6380 (mmm) REVERT: E 125 CYS cc_start: 0.6907 (m) cc_final: 0.6356 (m) REVERT: E 140 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8308 (tptt) REVERT: E 141 ILE cc_start: 0.8455 (tp) cc_final: 0.8109 (tp) REVERT: E 186 TRP cc_start: 0.8575 (t60) cc_final: 0.7945 (t60) REVERT: E 194 GLU cc_start: 0.8506 (pp20) cc_final: 0.8155 (pp20) REVERT: E 197 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8063 (mtm110) REVERT: E 216 ASP cc_start: 0.8464 (t0) cc_final: 0.8075 (t70) REVERT: E 220 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7780 (mtm-85) REVERT: E 250 LYS cc_start: 0.8421 (ttpp) cc_final: 0.7978 (mtpt) REVERT: F 69 LYS cc_start: 0.8284 (mppt) cc_final: 0.8052 (mmtp) REVERT: F 195 MET cc_start: 0.9064 (mpp) cc_final: 0.8757 (mpp) REVERT: F 218 ASP cc_start: 0.8506 (t0) cc_final: 0.8216 (t0) REVERT: F 246 ASN cc_start: 0.9053 (t0) cc_final: 0.8659 (t0) REVERT: F 320 TYR cc_start: 0.8210 (p90) cc_final: 0.7667 (p90) REVERT: F 321 LYS cc_start: 0.9383 (mtmm) cc_final: 0.9178 (mtmm) REVERT: F 340 LYS cc_start: 0.9336 (tttp) cc_final: 0.8871 (ttpp) REVERT: F 367 VAL cc_start: 0.9014 (t) cc_final: 0.8633 (m) REVERT: F 374 THR cc_start: 0.7752 (m) cc_final: 0.7328 (p) REVERT: F 394 VAL cc_start: 0.9345 (t) cc_final: 0.8959 (p) REVERT: F 397 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7056 (tt0) REVERT: F 433 MET cc_start: 0.7524 (mmt) cc_final: 0.7225 (tpp) REVERT: G 20 ARG cc_start: 0.8861 (tpt90) cc_final: 0.8647 (tpt90) REVERT: G 168 MET cc_start: 0.7973 (mtp) cc_final: 0.7425 (mtm) REVERT: G 327 GLU cc_start: 0.8030 (tt0) cc_final: 0.7380 (tt0) REVERT: G 347 ASP cc_start: 0.8288 (t0) cc_final: 0.7932 (t0) REVERT: G 360 TYR cc_start: 0.8847 (t80) cc_final: 0.8076 (t80) REVERT: G 362 ARG cc_start: 0.9238 (mtp180) cc_final: 0.8987 (mtm-85) REVERT: G 367 THR cc_start: 0.9083 (m) cc_final: 0.8825 (p) REVERT: H 20 LEU cc_start: 0.8071 (mt) cc_final: 0.7260 (tt) REVERT: H 28 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7687 (mm110) REVERT: H 67 ASN cc_start: 0.8478 (t0) cc_final: 0.8221 (t0) REVERT: H 97 VAL cc_start: 0.9246 (m) cc_final: 0.8923 (p) REVERT: H 99 LEU cc_start: 0.8815 (mp) cc_final: 0.8613 (mp) REVERT: H 109 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7218 (mm-30) REVERT: I 125 CYS cc_start: 0.8726 (t) cc_final: 0.8485 (t) REVERT: I 143 ASN cc_start: 0.8723 (t0) cc_final: 0.8392 (t0) REVERT: I 156 MET cc_start: 0.8784 (ppp) cc_final: 0.8535 (ppp) REVERT: I 193 TYR cc_start: 0.8317 (t80) cc_final: 0.7848 (t80) REVERT: I 198 PHE cc_start: 0.8959 (m-10) cc_final: 0.8730 (m-10) REVERT: I 222 VAL cc_start: 0.9075 (t) cc_final: 0.8803 (m) REVERT: I 243 ASN cc_start: 0.8299 (t0) cc_final: 0.7777 (m-40) REVERT: J 57 SER cc_start: 0.9223 (m) cc_final: 0.8315 (p) REVERT: J 251 LEU cc_start: 0.9364 (tp) cc_final: 0.9046 (tp) REVERT: J 262 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8296 (mm-30) REVERT: J 273 TYR cc_start: 0.7945 (p90) cc_final: 0.7431 (p90) REVERT: J 366 ILE cc_start: 0.9393 (mt) cc_final: 0.8989 (tp) REVERT: J 390 GLU cc_start: 0.8626 (tt0) cc_final: 0.7987 (tm-30) REVERT: J 396 GLN cc_start: 0.8269 (pm20) cc_final: 0.8060 (pm20) REVERT: J 404 LYS cc_start: 0.8968 (mppt) cc_final: 0.8620 (tppt) REVERT: K 54 ASN cc_start: 0.8037 (p0) cc_final: 0.7788 (p0) REVERT: K 96 HIS cc_start: 0.7898 (p90) cc_final: 0.7448 (p-80) REVERT: K 97 LYS cc_start: 0.8648 (tptp) cc_final: 0.8433 (tptt) REVERT: K 104 GLN cc_start: 0.8822 (tp40) cc_final: 0.8564 (tp40) REVERT: K 137 ARG cc_start: 0.8436 (mtp-110) cc_final: 0.7841 (mtp-110) REVERT: K 141 LEU cc_start: 0.9470 (tp) cc_final: 0.9112 (tt) REVERT: K 156 ASP cc_start: 0.8447 (t0) cc_final: 0.7936 (t0) REVERT: K 158 LEU cc_start: 0.9089 (mt) cc_final: 0.8415 (mt) REVERT: K 235 LYS cc_start: 0.5425 (tttm) cc_final: 0.5095 (tptm) REVERT: K 305 ASP cc_start: 0.8565 (t0) cc_final: 0.8275 (t0) REVERT: K 330 TRP cc_start: 0.9350 (t-100) cc_final: 0.9011 (t-100) REVERT: K 360 TYR cc_start: 0.9055 (t80) cc_final: 0.8515 (t80) REVERT: L 20 LEU cc_start: 0.7337 (mt) cc_final: 0.7049 (mp) REVERT: L 26 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8472 (tm-30) REVERT: L 28 GLN cc_start: 0.7530 (mm110) cc_final: 0.7153 (mm110) REVERT: L 43 LEU cc_start: 0.8717 (mt) cc_final: 0.8488 (mt) REVERT: L 80 ASP cc_start: 0.8067 (t0) cc_final: 0.7585 (t0) REVERT: L 92 VAL cc_start: 0.8551 (t) cc_final: 0.8170 (t) REVERT: L 101 ASN cc_start: 0.8784 (t0) cc_final: 0.7836 (m110) REVERT: L 104 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6755 (tm-30) REVERT: L 105 LEU cc_start: 0.8164 (tp) cc_final: 0.7949 (tp) REVERT: L 106 PHE cc_start: 0.7784 (m-80) cc_final: 0.7334 (m-10) REVERT: L 109 GLU cc_start: 0.8551 (tt0) cc_final: 0.8204 (pm20) REVERT: L 111 GLU cc_start: 0.8799 (tt0) cc_final: 0.8511 (mm-30) REVERT: M 110 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7392 (tttm) REVERT: M 125 CYS cc_start: 0.7949 (t) cc_final: 0.7513 (t) REVERT: M 133 LYS cc_start: 0.8016 (pttp) cc_final: 0.7291 (pptt) REVERT: M 176 THR cc_start: 0.7544 (t) cc_final: 0.5752 (t) REVERT: M 178 ASP cc_start: 0.8317 (p0) cc_final: 0.7914 (p0) REVERT: M 195 ASN cc_start: 0.8814 (m-40) cc_final: 0.8563 (m-40) REVERT: M 202 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8032 (ttt90) REVERT: M 220 ARG cc_start: 0.8677 (mtm180) cc_final: 0.8139 (mtm180) REVERT: N 144 LEU cc_start: 0.8707 (mt) cc_final: 0.8413 (mt) REVERT: N 187 TYR cc_start: 0.8991 (t80) cc_final: 0.8624 (t80) REVERT: N 321 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8794 (mtmt) REVERT: N 396 GLN cc_start: 0.9274 (tt0) cc_final: 0.8900 (tt0) REVERT: O 34 VAL cc_start: 0.9654 (t) cc_final: 0.9395 (m) REVERT: O 67 MET cc_start: 0.8410 (tpp) cc_final: 0.8108 (tpp) REVERT: O 80 MET cc_start: 0.9204 (mmp) cc_final: 0.8515 (mmm) REVERT: O 125 THR cc_start: 0.9405 (m) cc_final: 0.8896 (p) REVERT: O 165 TYR cc_start: 0.8553 (p90) cc_final: 0.8189 (p90) REVERT: O 233 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7700 (tp-100) REVERT: P 48 LEU cc_start: 0.9414 (mt) cc_final: 0.9166 (mt) REVERT: P 55 THR cc_start: 0.9347 (p) cc_final: 0.9126 (p) REVERT: P 80 ASP cc_start: 0.8090 (m-30) cc_final: 0.7774 (m-30) REVERT: P 98 PHE cc_start: 0.8292 (p90) cc_final: 0.8048 (p90) REVERT: Q 29 GLU cc_start: 0.8790 (tp30) cc_final: 0.8468 (mt-10) REVERT: Q 55 THR cc_start: 0.8557 (p) cc_final: 0.8140 (t) REVERT: Q 77 GLU cc_start: 0.8472 (tp30) cc_final: 0.7751 (pt0) REVERT: Q 104 GLU cc_start: 0.6749 (mp0) cc_final: 0.6496 (mp0) REVERT: R 115 MET cc_start: 0.8636 (mmm) cc_final: 0.8266 (mmm) REVERT: R 125 CYS cc_start: 0.9067 (t) cc_final: 0.8317 (t) REVERT: R 126 VAL cc_start: 0.9427 (m) cc_final: 0.9182 (m) REVERT: R 127 VAL cc_start: 0.9220 (t) cc_final: 0.8993 (m) REVERT: R 130 ARG cc_start: 0.8818 (ptp-110) cc_final: 0.8224 (ptp-170) REVERT: R 133 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8510 (tttt) REVERT: R 143 ASN cc_start: 0.6444 (m-40) cc_final: 0.6018 (t0) REVERT: R 160 GLU cc_start: 0.8397 (mp0) cc_final: 0.7822 (mp0) REVERT: R 186 TRP cc_start: 0.7917 (t60) cc_final: 0.7539 (t60) REVERT: R 191 VAL cc_start: 0.8455 (m) cc_final: 0.8252 (p) REVERT: R 193 TYR cc_start: 0.8561 (t80) cc_final: 0.8286 (t80) REVERT: R 194 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7244 (tm-30) REVERT: R 202 ARG cc_start: 0.8583 (ttt-90) cc_final: 0.8176 (tpt-90) REVERT: R 209 ASP cc_start: 0.8218 (m-30) cc_final: 0.7646 (t0) outliers start: 5 outliers final: 2 residues processed: 949 average time/residue: 0.4666 time to fit residues: 715.1538 Evaluate side-chains 777 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 775 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 193 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 371 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 273 optimal weight: 7.9990 chunk 264 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 100 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS E 243 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS G 174 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 ASN J 399 GLN N 319 GLN ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 353 HIS P 94 HIS R 143 ASN R 192 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102967 restraints weight = 75933.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106873 restraints weight = 38114.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108296 restraints weight = 21344.037| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34852 Z= 0.149 Angle : 0.621 10.556 47484 Z= 0.324 Chirality : 0.046 0.203 5340 Planarity : 0.004 0.058 6104 Dihedral : 5.101 24.774 4744 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.37 (0.13), residues: 4368 helix: 1.69 (0.24), residues: 495 sheet: -0.26 (0.14), residues: 1387 loop : -0.59 (0.13), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 279 HIS 0.007 0.001 HIS G 249 PHE 0.022 0.002 PHE J 398 TYR 0.022 0.002 TYR I 157 ARG 0.010 0.001 ARG O 303 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 1213) hydrogen bonds : angle 5.44120 ( 3426) SS BOND : bond 0.00370 ( 52) SS BOND : angle 1.39974 ( 104) covalent geometry : bond 0.00338 (34800) covalent geometry : angle 0.61829 (47380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 961 time to evaluate : 3.866 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8806 (p0) cc_final: 0.8419 (p0) REVERT: A 218 ASP cc_start: 0.8360 (t0) cc_final: 0.8002 (t0) REVERT: A 240 TYR cc_start: 0.9216 (t80) cc_final: 0.8666 (t80) REVERT: A 311 ASP cc_start: 0.8865 (p0) cc_final: 0.8530 (p0) REVERT: A 321 LYS cc_start: 0.9671 (mtpt) cc_final: 0.9329 (mtpp) REVERT: A 362 GLN cc_start: 0.8799 (pt0) cc_final: 0.8517 (pt0) REVERT: A 390 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8236 (pt0) REVERT: A 433 MET cc_start: 0.7739 (mmp) cc_final: 0.7496 (tpt) REVERT: B 76 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8510 (mttp) REVERT: B 80 MET cc_start: 0.7579 (mmt) cc_final: 0.6676 (mmm) REVERT: B 156 ASP cc_start: 0.7804 (t0) cc_final: 0.7554 (t0) REVERT: B 239 ASN cc_start: 0.8958 (t0) cc_final: 0.8667 (t0) REVERT: E 125 CYS cc_start: 0.6850 (m) cc_final: 0.6275 (m) REVERT: E 140 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8299 (tmtt) REVERT: E 141 ILE cc_start: 0.8530 (tp) cc_final: 0.8320 (tp) REVERT: E 186 TRP cc_start: 0.8548 (t60) cc_final: 0.7854 (t60) REVERT: E 194 GLU cc_start: 0.8653 (pp20) cc_final: 0.8173 (pp20) REVERT: E 197 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8157 (mtm110) REVERT: F 66 LEU cc_start: 0.7930 (mt) cc_final: 0.7333 (mp) REVERT: F 69 LYS cc_start: 0.8189 (mppt) cc_final: 0.7953 (mmtp) REVERT: F 160 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8738 (tppt) REVERT: F 195 MET cc_start: 0.9072 (mpp) cc_final: 0.8499 (mpp) REVERT: F 218 ASP cc_start: 0.8522 (t0) cc_final: 0.8180 (t0) REVERT: F 289 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8424 (tpp80) REVERT: F 320 TYR cc_start: 0.8163 (p90) cc_final: 0.7696 (p90) REVERT: F 340 LYS cc_start: 0.9315 (tttp) cc_final: 0.8844 (ttpp) REVERT: F 367 VAL cc_start: 0.9051 (t) cc_final: 0.8771 (m) REVERT: F 394 VAL cc_start: 0.9368 (t) cc_final: 0.8991 (p) REVERT: F 397 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7239 (tt0) REVERT: F 433 MET cc_start: 0.7500 (mmt) cc_final: 0.7291 (tpp) REVERT: G 20 ARG cc_start: 0.8906 (tpt90) cc_final: 0.8639 (tpt90) REVERT: G 168 MET cc_start: 0.7974 (mtp) cc_final: 0.7454 (mtm) REVERT: G 279 TRP cc_start: 0.8710 (p-90) cc_final: 0.8419 (p-90) REVERT: G 327 GLU cc_start: 0.7956 (tt0) cc_final: 0.7328 (tt0) REVERT: G 347 ASP cc_start: 0.8045 (t0) cc_final: 0.7694 (t0) REVERT: G 393 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7536 (tpp80) REVERT: H 20 LEU cc_start: 0.8075 (mt) cc_final: 0.7279 (tt) REVERT: H 28 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7571 (mm110) REVERT: H 67 ASN cc_start: 0.8396 (t0) cc_final: 0.8182 (t0) REVERT: H 97 VAL cc_start: 0.9321 (m) cc_final: 0.8980 (p) REVERT: H 100 GLU cc_start: 0.8168 (pp20) cc_final: 0.7965 (pp20) REVERT: H 109 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7039 (mm-30) REVERT: H 111 GLU cc_start: 0.2664 (tp30) cc_final: 0.2298 (tp30) REVERT: I 125 CYS cc_start: 0.8841 (t) cc_final: 0.8638 (t) REVERT: I 156 MET cc_start: 0.8428 (ppp) cc_final: 0.8171 (ppp) REVERT: I 160 GLU cc_start: 0.8087 (pm20) cc_final: 0.7816 (pm20) REVERT: I 193 TYR cc_start: 0.8382 (t80) cc_final: 0.7763 (t80) REVERT: I 198 PHE cc_start: 0.8887 (m-10) cc_final: 0.8632 (m-10) REVERT: I 222 VAL cc_start: 0.9049 (t) cc_final: 0.8737 (m) REVERT: I 243 ASN cc_start: 0.8117 (t0) cc_final: 0.7589 (m-40) REVERT: J 57 SER cc_start: 0.9157 (m) cc_final: 0.8097 (p) REVERT: J 251 LEU cc_start: 0.9334 (tp) cc_final: 0.9077 (tp) REVERT: J 257 PHE cc_start: 0.8742 (m-10) cc_final: 0.8534 (m-10) REVERT: J 262 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8146 (mp0) REVERT: J 366 ILE cc_start: 0.9334 (mt) cc_final: 0.8954 (tp) REVERT: J 390 GLU cc_start: 0.8600 (tt0) cc_final: 0.7955 (tm-30) REVERT: J 396 GLN cc_start: 0.8280 (pm20) cc_final: 0.8067 (pm20) REVERT: J 399 GLN cc_start: 0.8237 (mm110) cc_final: 0.7244 (pp30) REVERT: J 404 LYS cc_start: 0.8989 (mppt) cc_final: 0.8624 (tppt) REVERT: K 30 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9114 (tttm) REVERT: K 46 GLN cc_start: 0.8021 (tt0) cc_final: 0.7496 (tt0) REVERT: K 54 ASN cc_start: 0.7951 (p0) cc_final: 0.7723 (p0) REVERT: K 97 LYS cc_start: 0.8493 (tptp) cc_final: 0.8256 (tptt) REVERT: K 141 LEU cc_start: 0.9462 (tp) cc_final: 0.9101 (tt) REVERT: K 156 ASP cc_start: 0.8433 (t0) cc_final: 0.7834 (t0) REVERT: K 158 LEU cc_start: 0.9217 (mt) cc_final: 0.8582 (mt) REVERT: K 235 LYS cc_start: 0.5202 (tttm) cc_final: 0.4717 (mmmt) REVERT: K 240 SER cc_start: 0.9145 (t) cc_final: 0.8943 (t) REVERT: K 305 ASP cc_start: 0.8464 (t0) cc_final: 0.8144 (t0) REVERT: K 330 TRP cc_start: 0.9298 (t-100) cc_final: 0.8778 (t-100) REVERT: L 20 LEU cc_start: 0.7542 (mt) cc_final: 0.7061 (mp) REVERT: L 26 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8469 (tm-30) REVERT: L 28 GLN cc_start: 0.7484 (mm110) cc_final: 0.7106 (mm110) REVERT: L 66 LEU cc_start: 0.7884 (tt) cc_final: 0.7640 (tt) REVERT: L 77 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8771 (mm-30) REVERT: L 80 ASP cc_start: 0.8112 (t0) cc_final: 0.7602 (t0) REVERT: L 92 VAL cc_start: 0.8516 (t) cc_final: 0.7892 (t) REVERT: L 101 ASN cc_start: 0.8963 (t0) cc_final: 0.8135 (m110) REVERT: L 104 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6792 (tm-30) REVERT: L 105 LEU cc_start: 0.8130 (tp) cc_final: 0.7860 (tp) REVERT: L 109 GLU cc_start: 0.8537 (tt0) cc_final: 0.8169 (pm20) REVERT: L 111 GLU cc_start: 0.8794 (tt0) cc_final: 0.8544 (tp30) REVERT: M 125 CYS cc_start: 0.7999 (t) cc_final: 0.7708 (t) REVERT: M 176 THR cc_start: 0.7158 (t) cc_final: 0.5412 (m) REVERT: M 178 ASP cc_start: 0.8323 (p0) cc_final: 0.7932 (p0) REVERT: M 202 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8202 (ttt90) REVERT: M 207 LYS cc_start: 0.8051 (tppt) cc_final: 0.7830 (tppt) REVERT: M 212 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7891 (mmm-85) REVERT: M 220 ARG cc_start: 0.8557 (mtm180) cc_final: 0.7583 (mtm180) REVERT: N 100 ASN cc_start: 0.8664 (m110) cc_final: 0.8453 (m110) REVERT: N 143 ARG cc_start: 0.8505 (ttm110) cc_final: 0.7950 (ttm-80) REVERT: N 144 LEU cc_start: 0.8662 (mt) cc_final: 0.8353 (mt) REVERT: N 187 TYR cc_start: 0.8882 (t80) cc_final: 0.8473 (t80) REVERT: N 321 LYS cc_start: 0.9170 (mtpp) cc_final: 0.8640 (mtpt) REVERT: N 396 GLN cc_start: 0.9174 (tt0) cc_final: 0.8849 (tt0) REVERT: O 34 VAL cc_start: 0.9654 (t) cc_final: 0.9383 (m) REVERT: O 42 SER cc_start: 0.9557 (m) cc_final: 0.9345 (m) REVERT: O 67 MET cc_start: 0.8295 (tpp) cc_final: 0.7968 (tpp) REVERT: O 80 MET cc_start: 0.9228 (mmp) cc_final: 0.8758 (mmt) REVERT: O 125 THR cc_start: 0.9342 (m) cc_final: 0.8759 (p) REVERT: O 165 TYR cc_start: 0.8579 (p90) cc_final: 0.8201 (p90) REVERT: O 230 LYS cc_start: 0.8875 (pttm) cc_final: 0.8662 (pmtt) REVERT: O 233 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7572 (tp-100) REVERT: O 239 ASN cc_start: 0.9149 (t0) cc_final: 0.8853 (t0) REVERT: O 242 ASP cc_start: 0.8523 (t0) cc_final: 0.8287 (t0) REVERT: P 48 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mt) REVERT: P 61 THR cc_start: 0.8559 (p) cc_final: 0.8223 (p) REVERT: P 80 ASP cc_start: 0.8145 (m-30) cc_final: 0.7895 (m-30) REVERT: P 98 PHE cc_start: 0.8266 (p90) cc_final: 0.8021 (p90) REVERT: Q 29 GLU cc_start: 0.8815 (tp30) cc_final: 0.8508 (mt-10) REVERT: Q 55 THR cc_start: 0.8459 (p) cc_final: 0.8122 (t) REVERT: Q 77 GLU cc_start: 0.8377 (tp30) cc_final: 0.7829 (pt0) REVERT: Q 99 LEU cc_start: 0.9014 (mt) cc_final: 0.8736 (mt) REVERT: Q 104 GLU cc_start: 0.6971 (mp0) cc_final: 0.6697 (mp0) REVERT: R 115 MET cc_start: 0.8617 (mmm) cc_final: 0.8308 (mmm) REVERT: R 125 CYS cc_start: 0.8943 (t) cc_final: 0.8131 (t) REVERT: R 126 VAL cc_start: 0.9434 (m) cc_final: 0.9195 (m) REVERT: R 127 VAL cc_start: 0.9195 (t) cc_final: 0.8938 (m) REVERT: R 143 ASN cc_start: 0.6042 (m110) cc_final: 0.5735 (t0) REVERT: R 158 ASP cc_start: 0.8703 (t0) cc_final: 0.8430 (t0) REVERT: R 160 GLU cc_start: 0.8431 (mp0) cc_final: 0.7840 (mp0) REVERT: R 191 VAL cc_start: 0.8507 (m) cc_final: 0.8279 (p) REVERT: R 193 TYR cc_start: 0.8495 (t80) cc_final: 0.8194 (t80) REVERT: R 194 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7202 (tm-30) REVERT: R 197 ARG cc_start: 0.9233 (ttm-80) cc_final: 0.8813 (tpp-160) REVERT: R 207 LYS cc_start: 0.9373 (tttm) cc_final: 0.8968 (tptt) REVERT: R 209 ASP cc_start: 0.8292 (m-30) cc_final: 0.7783 (t0) outliers start: 1 outliers final: 0 residues processed: 962 average time/residue: 0.4763 time to fit residues: 742.2856 Evaluate side-chains 787 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 787 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 201 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 429 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 chunk 417 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 327 HIS A 345 HIS ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS G 71 HIS G 174 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN I 188 HIS ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN R 192 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101325 restraints weight = 77704.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105354 restraints weight = 39574.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106270 restraints weight = 21988.074| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 34852 Z= 0.287 Angle : 0.707 20.548 47484 Z= 0.366 Chirality : 0.047 0.213 5340 Planarity : 0.005 0.060 6104 Dihedral : 5.273 26.586 4744 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.58 (0.13), residues: 4368 helix: 1.60 (0.23), residues: 495 sheet: -0.39 (0.14), residues: 1395 loop : -0.76 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 186 HIS 0.009 0.002 HIS N 125 PHE 0.025 0.002 PHE B 100 TYR 0.022 0.002 TYR J 107 ARG 0.010 0.001 ARG O 303 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1213) hydrogen bonds : angle 5.53761 ( 3426) SS BOND : bond 0.00361 ( 52) SS BOND : angle 1.64121 ( 104) covalent geometry : bond 0.00645 (34800) covalent geometry : angle 0.70346 (47380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 878 time to evaluate : 4.322 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: 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 2 GLU cc_start: 0.8997 (tt0) cc_final: 0.8706 (tp30) REVERT: A 88 MET cc_start: 0.8660 (mtm) cc_final: 0.8245 (mtp) REVERT: A 212 ASP cc_start: 0.8841 (p0) cc_final: 0.8408 (p0) REVERT: A 311 ASP cc_start: 0.8918 (p0) cc_final: 0.8638 (p0) REVERT: A 321 LYS cc_start: 0.9664 (mtpt) cc_final: 0.9447 (mtpp) REVERT: A 390 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8456 (pt0) REVERT: B 80 MET cc_start: 0.7475 (mmt) cc_final: 0.6787 (mmm) REVERT: B 239 ASN cc_start: 0.9050 (t0) cc_final: 0.8716 (t0) REVERT: E 125 CYS cc_start: 0.7080 (m) cc_final: 0.6629 (m) REVERT: E 140 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8285 (tmtt) REVERT: E 186 TRP cc_start: 0.8576 (t60) cc_final: 0.7870 (t60) REVERT: E 187 HIS cc_start: 0.8836 (t-90) cc_final: 0.8394 (t-90) REVERT: E 194 GLU cc_start: 0.8711 (pp20) cc_final: 0.8048 (pp20) REVERT: E 197 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8217 (mtm110) REVERT: E 250 LYS cc_start: 0.8381 (ttpp) cc_final: 0.7957 (mtpt) REVERT: F 69 LYS cc_start: 0.8076 (mppt) cc_final: 0.7774 (mmtp) REVERT: F 99 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6929 (tm-30) REVERT: F 160 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8723 (tppt) REVERT: F 195 MET cc_start: 0.8963 (mpp) cc_final: 0.8475 (mpp) REVERT: F 218 ASP cc_start: 0.8521 (t0) cc_final: 0.8256 (t0) REVERT: F 289 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8462 (tpp80) REVERT: F 320 TYR cc_start: 0.8169 (p90) cc_final: 0.7639 (p90) REVERT: F 340 LYS cc_start: 0.9368 (tttp) cc_final: 0.8891 (ttpp) REVERT: F 367 VAL cc_start: 0.9020 (t) cc_final: 0.8820 (m) REVERT: F 372 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8735 (ttpt) REVERT: F 394 VAL cc_start: 0.9430 (t) cc_final: 0.9035 (p) REVERT: F 433 MET cc_start: 0.7555 (mmt) cc_final: 0.7264 (tpp) REVERT: G 37 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8096 (tm-30) REVERT: G 279 TRP cc_start: 0.8946 (p-90) cc_final: 0.8459 (p-90) REVERT: G 327 GLU cc_start: 0.7996 (tt0) cc_final: 0.7475 (tt0) REVERT: G 347 ASP cc_start: 0.8167 (t0) cc_final: 0.7792 (t0) REVERT: G 360 TYR cc_start: 0.8708 (t80) cc_final: 0.8047 (t80) REVERT: G 393 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7366 (tpp80) REVERT: H 20 LEU cc_start: 0.8351 (mt) cc_final: 0.7553 (tt) REVERT: H 28 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7549 (mm110) REVERT: H 60 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7864 (ttm170) REVERT: H 67 ASN cc_start: 0.8398 (t0) cc_final: 0.8153 (t0) REVERT: H 97 VAL cc_start: 0.9279 (m) cc_final: 0.8983 (p) REVERT: H 99 LEU cc_start: 0.8812 (mp) cc_final: 0.8581 (mp) REVERT: H 111 GLU cc_start: 0.2835 (tp30) cc_final: 0.2327 (tp30) REVERT: I 125 CYS cc_start: 0.8803 (t) cc_final: 0.8593 (t) REVERT: I 143 ASN cc_start: 0.8834 (t0) cc_final: 0.8576 (t0) REVERT: I 160 GLU cc_start: 0.7953 (pm20) cc_final: 0.7618 (pm20) REVERT: I 174 GLN cc_start: 0.8901 (mm110) cc_final: 0.8680 (mm110) REVERT: I 193 TYR cc_start: 0.8571 (t80) cc_final: 0.7933 (t80) REVERT: I 198 PHE cc_start: 0.8899 (m-10) cc_final: 0.8682 (m-10) REVERT: I 220 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7342 (mtm-85) REVERT: I 243 ASN cc_start: 0.8336 (t0) cc_final: 0.7812 (m-40) REVERT: I 249 ILE cc_start: 0.8343 (mt) cc_final: 0.8084 (tp) REVERT: J 57 SER cc_start: 0.9177 (m) cc_final: 0.8273 (p) REVERT: J 251 LEU cc_start: 0.9346 (tp) cc_final: 0.9112 (tp) REVERT: J 366 ILE cc_start: 0.9423 (mt) cc_final: 0.9017 (tp) REVERT: J 390 GLU cc_start: 0.8645 (tt0) cc_final: 0.8223 (tm-30) REVERT: J 404 LYS cc_start: 0.9004 (mppt) cc_final: 0.8738 (tppt) REVERT: K 54 ASN cc_start: 0.7987 (p0) cc_final: 0.7724 (p0) REVERT: K 55 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8123 (tm-30) REVERT: K 97 LYS cc_start: 0.8866 (tptp) cc_final: 0.8607 (tptt) REVERT: K 137 ARG cc_start: 0.8695 (mtp-110) cc_final: 0.8188 (mtp-110) REVERT: K 156 ASP cc_start: 0.8540 (t0) cc_final: 0.8256 (t0) REVERT: K 305 ASP cc_start: 0.8576 (t0) cc_final: 0.8287 (t0) REVERT: K 330 TRP cc_start: 0.9323 (t-100) cc_final: 0.8890 (t-100) REVERT: K 334 GLU cc_start: 0.8590 (mp0) cc_final: 0.8174 (mp0) REVERT: L 20 LEU cc_start: 0.7646 (mt) cc_final: 0.7093 (mp) REVERT: L 26 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8504 (tm-30) REVERT: L 27 GLU cc_start: 0.8999 (tp30) cc_final: 0.8747 (tp30) REVERT: L 28 GLN cc_start: 0.7696 (mm110) cc_final: 0.7149 (mm110) REVERT: L 43 LEU cc_start: 0.8755 (mt) cc_final: 0.8465 (mt) REVERT: L 80 ASP cc_start: 0.8116 (t0) cc_final: 0.7635 (t0) REVERT: L 92 VAL cc_start: 0.8575 (t) cc_final: 0.8088 (t) REVERT: L 101 ASN cc_start: 0.9021 (t0) cc_final: 0.8130 (m-40) REVERT: L 104 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6553 (tm-30) REVERT: L 105 LEU cc_start: 0.8172 (tp) cc_final: 0.7844 (tp) REVERT: L 106 PHE cc_start: 0.7555 (m-80) cc_final: 0.7126 (m-10) REVERT: L 109 GLU cc_start: 0.8550 (tt0) cc_final: 0.8229 (pm20) REVERT: L 111 GLU cc_start: 0.8747 (tt0) cc_final: 0.8494 (mm-30) REVERT: M 125 CYS cc_start: 0.7928 (t) cc_final: 0.7694 (t) REVERT: M 133 LYS cc_start: 0.8073 (pttp) cc_final: 0.7353 (pptt) REVERT: M 135 LEU cc_start: 0.9286 (tp) cc_final: 0.8987 (tp) REVERT: M 176 THR cc_start: 0.7532 (t) cc_final: 0.6392 (t) REVERT: M 178 ASP cc_start: 0.8454 (p0) cc_final: 0.8217 (p0) REVERT: M 195 ASN cc_start: 0.8863 (m-40) cc_final: 0.8629 (m110) REVERT: M 198 PHE cc_start: 0.8855 (m-10) cc_final: 0.8644 (m-10) REVERT: M 202 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8181 (ttt90) REVERT: M 220 ARG cc_start: 0.8613 (mtm180) cc_final: 0.8175 (mtm180) REVERT: N 144 LEU cc_start: 0.8624 (mt) cc_final: 0.8376 (mt) REVERT: N 187 TYR cc_start: 0.8917 (t80) cc_final: 0.8540 (t80) REVERT: N 321 LYS cc_start: 0.9240 (mtpp) cc_final: 0.8807 (mtmm) REVERT: N 396 GLN cc_start: 0.9251 (tt0) cc_final: 0.9007 (tt0) REVERT: O 34 VAL cc_start: 0.9604 (t) cc_final: 0.9317 (m) REVERT: O 67 MET cc_start: 0.8503 (tpp) cc_final: 0.8100 (tpp) REVERT: O 80 MET cc_start: 0.9281 (mmp) cc_final: 0.8896 (mmp) REVERT: O 125 THR cc_start: 0.9401 (m) cc_final: 0.8876 (p) REVERT: O 165 TYR cc_start: 0.8581 (p90) cc_final: 0.8188 (p90) REVERT: O 233 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7536 (tm-30) REVERT: O 242 ASP cc_start: 0.8503 (t0) cc_final: 0.8244 (t0) REVERT: P 80 ASP cc_start: 0.8345 (m-30) cc_final: 0.8013 (m-30) REVERT: P 104 GLU cc_start: 0.6806 (mp0) cc_final: 0.6584 (mp0) REVERT: Q 29 GLU cc_start: 0.8952 (tp30) cc_final: 0.8567 (mt-10) REVERT: Q 55 THR cc_start: 0.8399 (p) cc_final: 0.7989 (t) REVERT: Q 77 GLU cc_start: 0.8415 (tp30) cc_final: 0.7686 (pt0) REVERT: Q 99 LEU cc_start: 0.9019 (mt) cc_final: 0.8792 (mt) REVERT: Q 104 GLU cc_start: 0.7059 (mp0) cc_final: 0.6663 (mp0) REVERT: R 115 MET cc_start: 0.8637 (mmm) cc_final: 0.8424 (mmm) REVERT: R 116 LEU cc_start: 0.9198 (tp) cc_final: 0.8880 (tp) REVERT: R 125 CYS cc_start: 0.9013 (t) cc_final: 0.8294 (t) REVERT: R 127 VAL cc_start: 0.9246 (t) cc_final: 0.9005 (m) REVERT: R 131 LEU cc_start: 0.9351 (tp) cc_final: 0.9126 (tp) REVERT: R 160 GLU cc_start: 0.8470 (mp0) cc_final: 0.7847 (mp0) REVERT: R 191 VAL cc_start: 0.8278 (m) cc_final: 0.8076 (p) REVERT: R 192 GLN cc_start: 0.8896 (pt0) cc_final: 0.8692 (pt0) REVERT: R 193 TYR cc_start: 0.8378 (t80) cc_final: 0.8091 (t80) REVERT: R 197 ARG cc_start: 0.9242 (ttm-80) cc_final: 0.8803 (tpp-160) REVERT: R 207 LYS cc_start: 0.9420 (tttm) cc_final: 0.9027 (tptt) REVERT: R 209 ASP cc_start: 0.8425 (m-30) cc_final: 0.7779 (t0) REVERT: R 212 ARG cc_start: 0.8465 (tpp-160) cc_final: 0.8209 (mmt-90) REVERT: R 250 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7194 (mttt) outliers start: 1 outliers final: 0 residues processed: 879 average time/residue: 0.6129 time to fit residues: 887.8639 Evaluate side-chains 753 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 753 time to evaluate : 5.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 43 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 chunk 284 optimal weight: 0.4980 chunk 94 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 360 optimal weight: 0.8980 chunk 99 optimal weight: 0.0470 chunk 336 optimal weight: 7.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 333 HIS B 50 GLN B 146 HIS ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 188 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS G 174 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 HIS ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN ** O 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 272 HIS R 143 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107015 restraints weight = 76728.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110977 restraints weight = 39092.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112089 restraints weight = 21861.653| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34852 Z= 0.114 Angle : 0.625 15.067 47484 Z= 0.321 Chirality : 0.046 0.197 5340 Planarity : 0.004 0.059 6104 Dihedral : 4.955 28.362 4744 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.37 (0.13), residues: 4368 helix: 1.62 (0.24), residues: 495 sheet: -0.23 (0.13), residues: 1455 loop : -0.60 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 186 HIS 0.007 0.001 HIS O 73 PHE 0.024 0.001 PHE P 98 TYR 0.022 0.001 TYR H 63 ARG 0.012 0.001 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 1213) hydrogen bonds : angle 5.26118 ( 3426) SS BOND : bond 0.00363 ( 52) SS BOND : angle 1.60205 ( 104) covalent geometry : bond 0.00260 (34800) covalent geometry : angle 0.62144 (47380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 933 time to evaluate : 3.636 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: 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: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8825 (mtm) cc_final: 0.8356 (mtp) REVERT: A 212 ASP cc_start: 0.8805 (p0) cc_final: 0.8359 (p0) REVERT: A 240 TYR cc_start: 0.8970 (t80) cc_final: 0.8617 (t80) REVERT: A 311 ASP cc_start: 0.8810 (p0) cc_final: 0.8511 (p0) REVERT: A 321 LYS cc_start: 0.9631 (mtpt) cc_final: 0.9421 (mtpp) REVERT: A 390 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8474 (pt0) REVERT: B 15 PHE cc_start: 0.7597 (t80) cc_final: 0.7323 (t80) REVERT: B 80 MET cc_start: 0.7566 (mmt) cc_final: 0.6760 (mmm) REVERT: B 156 ASP cc_start: 0.7797 (t0) cc_final: 0.7427 (t0) REVERT: B 168 MET cc_start: 0.9012 (mtp) cc_final: 0.8610 (mtp) REVERT: B 239 ASN cc_start: 0.9016 (t0) cc_final: 0.8629 (m-40) REVERT: E 123 TYR cc_start: 0.7880 (m-80) cc_final: 0.7500 (m-80) REVERT: E 125 CYS cc_start: 0.7014 (m) cc_final: 0.6587 (m) REVERT: E 140 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8355 (tmtt) REVERT: E 186 TRP cc_start: 0.8141 (t60) cc_final: 0.7524 (t60) REVERT: E 197 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8305 (mtm110) REVERT: E 212 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6861 (mmt90) REVERT: E 220 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8120 (mtm-85) REVERT: E 250 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8038 (mtpt) REVERT: F 43 ASN cc_start: 0.8908 (t0) cc_final: 0.8672 (t0) REVERT: F 66 LEU cc_start: 0.7697 (mt) cc_final: 0.7321 (mp) REVERT: F 99 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7106 (tm-30) REVERT: F 160 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8717 (tppt) REVERT: F 195 MET cc_start: 0.8979 (mpp) cc_final: 0.8336 (mpp) REVERT: F 218 ASP cc_start: 0.8488 (t0) cc_final: 0.8188 (t0) REVERT: F 320 TYR cc_start: 0.8064 (p90) cc_final: 0.7588 (p90) REVERT: F 340 LYS cc_start: 0.9388 (tttp) cc_final: 0.8925 (ttpp) REVERT: F 367 VAL cc_start: 0.9031 (t) cc_final: 0.8813 (m) REVERT: F 372 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8790 (ttpt) REVERT: F 394 VAL cc_start: 0.9384 (t) cc_final: 0.8989 (p) REVERT: F 433 MET cc_start: 0.7508 (mmt) cc_final: 0.7248 (tpp) REVERT: G 37 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8022 (tm-30) REVERT: G 145 VAL cc_start: 0.9218 (m) cc_final: 0.9005 (p) REVERT: G 168 MET cc_start: 0.8008 (mtp) cc_final: 0.7517 (mtm) REVERT: G 279 TRP cc_start: 0.8913 (p-90) cc_final: 0.8576 (p-90) REVERT: G 280 PHE cc_start: 0.8987 (t80) cc_final: 0.8787 (t80) REVERT: G 327 GLU cc_start: 0.7913 (tt0) cc_final: 0.7427 (tt0) REVERT: G 347 ASP cc_start: 0.8158 (t0) cc_final: 0.7818 (t0) REVERT: G 393 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7397 (tpp80) REVERT: H 28 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7543 (mm110) REVERT: H 60 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7849 (ttm170) REVERT: H 67 ASN cc_start: 0.8441 (t0) cc_final: 0.8234 (t0) REVERT: H 97 VAL cc_start: 0.9308 (m) cc_final: 0.8973 (p) REVERT: H 99 LEU cc_start: 0.8623 (mp) cc_final: 0.8155 (mp) REVERT: I 160 GLU cc_start: 0.7940 (pm20) cc_final: 0.7530 (pm20) REVERT: I 164 VAL cc_start: 0.8864 (t) cc_final: 0.8593 (m) REVERT: I 174 GLN cc_start: 0.8869 (mm110) cc_final: 0.8602 (mm110) REVERT: I 193 TYR cc_start: 0.8421 (t80) cc_final: 0.7733 (t80) REVERT: I 198 PHE cc_start: 0.8850 (m-10) cc_final: 0.8407 (m-10) REVERT: I 214 ILE cc_start: 0.9074 (mp) cc_final: 0.8831 (pt) REVERT: I 222 VAL cc_start: 0.9002 (t) cc_final: 0.8690 (t) REVERT: I 243 ASN cc_start: 0.8179 (t0) cc_final: 0.7667 (m-40) REVERT: J 195 MET cc_start: 0.8881 (mpp) cc_final: 0.8589 (mpp) REVERT: J 251 LEU cc_start: 0.9307 (tp) cc_final: 0.9032 (tp) REVERT: J 257 PHE cc_start: 0.8690 (m-10) cc_final: 0.8462 (m-10) REVERT: J 366 ILE cc_start: 0.9383 (mt) cc_final: 0.9016 (tp) REVERT: J 390 GLU cc_start: 0.8661 (tt0) cc_final: 0.8233 (tm-30) REVERT: J 399 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7592 (pp30) REVERT: J 404 LYS cc_start: 0.8987 (mppt) cc_final: 0.8643 (tppt) REVERT: K 54 ASN cc_start: 0.7865 (p0) cc_final: 0.7584 (p0) REVERT: K 55 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8096 (tm-30) REVERT: K 97 LYS cc_start: 0.8566 (tptp) cc_final: 0.8231 (tptt) REVERT: K 141 LEU cc_start: 0.9471 (tp) cc_final: 0.9031 (tt) REVERT: K 156 ASP cc_start: 0.8445 (t0) cc_final: 0.8062 (t0) REVERT: K 158 LEU cc_start: 0.9240 (mt) cc_final: 0.8635 (mt) REVERT: K 305 ASP cc_start: 0.8514 (t0) cc_final: 0.8163 (t0) REVERT: K 330 TRP cc_start: 0.9213 (t-100) cc_final: 0.8738 (t-100) REVERT: L 20 LEU cc_start: 0.7487 (mt) cc_final: 0.6999 (mp) REVERT: L 26 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8447 (tm-30) REVERT: L 27 GLU cc_start: 0.8997 (tp30) cc_final: 0.8723 (tp30) REVERT: L 28 GLN cc_start: 0.7625 (mm110) cc_final: 0.7078 (mm110) REVERT: L 54 GLN cc_start: 0.7911 (pm20) cc_final: 0.7351 (pm20) REVERT: L 80 ASP cc_start: 0.8168 (t0) cc_final: 0.7723 (t0) REVERT: L 92 VAL cc_start: 0.8614 (t) cc_final: 0.7994 (t) REVERT: L 101 ASN cc_start: 0.9000 (t0) cc_final: 0.8100 (m-40) REVERT: L 104 GLU cc_start: 0.7280 (tm-30) cc_final: 0.7048 (tm-30) REVERT: L 109 GLU cc_start: 0.8608 (tt0) cc_final: 0.8270 (pm20) REVERT: L 111 GLU cc_start: 0.8687 (tt0) cc_final: 0.8459 (tp30) REVERT: M 125 CYS cc_start: 0.7940 (t) cc_final: 0.7716 (t) REVERT: M 176 THR cc_start: 0.7150 (t) cc_final: 0.5138 (m) REVERT: M 178 ASP cc_start: 0.8367 (p0) cc_final: 0.8161 (p0) REVERT: M 193 TYR cc_start: 0.7213 (t80) cc_final: 0.6995 (t80) REVERT: M 194 GLU cc_start: 0.7484 (pp20) cc_final: 0.7006 (pp20) REVERT: M 195 ASN cc_start: 0.8846 (m-40) cc_final: 0.8611 (m110) REVERT: M 202 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8207 (ttt90) REVERT: M 220 ARG cc_start: 0.8553 (mtm180) cc_final: 0.7646 (mtm180) REVERT: N 143 ARG cc_start: 0.8477 (ttm110) cc_final: 0.7857 (ttm-80) REVERT: N 144 LEU cc_start: 0.8686 (mt) cc_final: 0.8362 (mt) REVERT: N 187 TYR cc_start: 0.8807 (t80) cc_final: 0.8359 (t80) REVERT: N 321 LYS cc_start: 0.9185 (mtpp) cc_final: 0.8791 (mtmm) REVERT: N 396 GLN cc_start: 0.9144 (tt0) cc_final: 0.8877 (tt0) REVERT: O 20 ARG cc_start: 0.8827 (tpt-90) cc_final: 0.8380 (tpp80) REVERT: O 34 VAL cc_start: 0.9592 (t) cc_final: 0.9320 (m) REVERT: O 67 MET cc_start: 0.8340 (tpp) cc_final: 0.7975 (tpp) REVERT: O 80 MET cc_start: 0.9263 (mmp) cc_final: 0.8817 (mmt) REVERT: O 125 THR cc_start: 0.9317 (m) cc_final: 0.8776 (p) REVERT: O 165 TYR cc_start: 0.8563 (p90) cc_final: 0.8357 (p90) REVERT: O 230 LYS cc_start: 0.8893 (pttt) cc_final: 0.8589 (pmtt) REVERT: O 233 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7420 (tp-100) REVERT: O 239 ASN cc_start: 0.9151 (t0) cc_final: 0.8848 (t0) REVERT: P 80 ASP cc_start: 0.8432 (m-30) cc_final: 0.8187 (m-30) REVERT: P 104 GLU cc_start: 0.6927 (mp0) cc_final: 0.6703 (mp0) REVERT: Q 77 GLU cc_start: 0.8214 (tp30) cc_final: 0.7697 (pt0) REVERT: Q 99 LEU cc_start: 0.9040 (mt) cc_final: 0.8782 (mt) REVERT: Q 104 GLU cc_start: 0.7234 (mp0) cc_final: 0.6941 (mp0) REVERT: R 125 CYS cc_start: 0.8907 (t) cc_final: 0.8110 (t) REVERT: R 126 VAL cc_start: 0.9398 (m) cc_final: 0.9084 (m) REVERT: R 127 VAL cc_start: 0.9172 (t) cc_final: 0.8961 (m) REVERT: R 133 LYS cc_start: 0.8590 (tmmt) cc_final: 0.8377 (tmtt) REVERT: R 143 ASN cc_start: 0.6271 (m-40) cc_final: 0.5761 (t0) REVERT: R 160 GLU cc_start: 0.8411 (mp0) cc_final: 0.7806 (mp0) REVERT: R 191 VAL cc_start: 0.8569 (m) cc_final: 0.8304 (p) REVERT: R 192 GLN cc_start: 0.8910 (pt0) cc_final: 0.8691 (pt0) REVERT: R 193 TYR cc_start: 0.8318 (t80) cc_final: 0.7980 (t80) REVERT: R 197 ARG cc_start: 0.9254 (ttm-80) cc_final: 0.8853 (tpp-160) REVERT: R 207 LYS cc_start: 0.9309 (tttm) cc_final: 0.8935 (tptp) REVERT: R 209 ASP cc_start: 0.8230 (m-30) cc_final: 0.7725 (t0) REVERT: R 212 ARG cc_start: 0.8495 (tpp-160) cc_final: 0.8251 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 933 average time/residue: 0.4902 time to fit residues: 748.6310 Evaluate side-chains 772 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 772 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 107 optimal weight: 0.0010 chunk 19 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 100 optimal weight: 40.0000 chunk 377 optimal weight: 6.9990 chunk 330 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 186 optimal weight: 30.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 333 HIS A 355 HIS A 364 ASN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS E 243 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS G 174 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 GLN L 107 GLN Q 101 ASN R 143 ASN R 192 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100159 restraints weight = 78135.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104063 restraints weight = 40171.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105139 restraints weight = 22417.547| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 34852 Z= 0.314 Angle : 0.738 12.864 47484 Z= 0.384 Chirality : 0.048 0.211 5340 Planarity : 0.005 0.055 6104 Dihedral : 5.302 28.647 4744 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.60 (0.13), residues: 4368 helix: 1.51 (0.24), residues: 497 sheet: -0.40 (0.13), residues: 1473 loop : -0.76 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 186 HIS 0.007 0.001 HIS A 331 PHE 0.028 0.003 PHE P 53 TYR 0.026 0.002 TYR A 46 ARG 0.013 0.001 ARG O 303 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1213) hydrogen bonds : angle 5.51264 ( 3426) SS BOND : bond 0.00441 ( 52) SS BOND : angle 2.03831 ( 104) covalent geometry : bond 0.00704 (34800) covalent geometry : angle 0.73219 (47380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 873 time to evaluate : 3.741 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.9004 (tt0) cc_final: 0.8709 (tp30) REVERT: A 88 MET cc_start: 0.8734 (mtm) cc_final: 0.8241 (mtp) REVERT: A 212 ASP cc_start: 0.8840 (p0) cc_final: 0.8479 (p0) REVERT: A 311 ASP cc_start: 0.8851 (p0) cc_final: 0.8629 (p0) REVERT: A 321 LYS cc_start: 0.9659 (mtpt) cc_final: 0.9411 (mtpp) REVERT: A 390 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8598 (pt0) REVERT: B 80 MET cc_start: 0.7733 (mmt) cc_final: 0.6917 (mmm) REVERT: B 156 ASP cc_start: 0.7915 (t0) cc_final: 0.7671 (t0) REVERT: B 239 ASN cc_start: 0.9118 (t0) cc_final: 0.8747 (t0) REVERT: E 125 CYS cc_start: 0.7082 (m) cc_final: 0.6659 (m) REVERT: E 141 ILE cc_start: 0.8668 (tp) cc_final: 0.8348 (tp) REVERT: E 186 TRP cc_start: 0.8281 (t60) cc_final: 0.7766 (t60) REVERT: E 187 HIS cc_start: 0.8682 (t70) cc_final: 0.8384 (t-90) REVERT: E 192 GLN cc_start: 0.8728 (mt0) cc_final: 0.8356 (tp-100) REVERT: E 194 GLU cc_start: 0.8992 (pp20) cc_final: 0.7927 (pp20) REVERT: E 197 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.8434 (mtm110) REVERT: E 212 ARG cc_start: 0.7486 (mmm-85) cc_final: 0.6867 (mtt-85) REVERT: E 250 LYS cc_start: 0.8400 (ttpp) cc_final: 0.7937 (ttpt) REVERT: F 43 ASN cc_start: 0.8943 (t0) cc_final: 0.8702 (t0) REVERT: F 66 LEU cc_start: 0.8034 (mt) cc_final: 0.7526 (mp) REVERT: F 69 LYS cc_start: 0.8094 (mppt) cc_final: 0.7831 (mmtp) REVERT: F 99 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7037 (tm-30) REVERT: F 143 ARG cc_start: 0.9014 (mmt-90) cc_final: 0.8810 (mmt-90) REVERT: F 160 LYS cc_start: 0.8973 (ttpp) cc_final: 0.8730 (tppt) REVERT: F 195 MET cc_start: 0.8982 (mpp) cc_final: 0.8444 (mpp) REVERT: F 218 ASP cc_start: 0.8539 (t0) cc_final: 0.8273 (t0) REVERT: F 320 TYR cc_start: 0.8163 (p90) cc_final: 0.7665 (p90) REVERT: F 340 LYS cc_start: 0.9330 (tttp) cc_final: 0.8834 (ttpp) REVERT: F 367 VAL cc_start: 0.9041 (t) cc_final: 0.8831 (m) REVERT: F 394 VAL cc_start: 0.9341 (t) cc_final: 0.8934 (p) REVERT: F 433 MET cc_start: 0.7569 (mmt) cc_final: 0.7276 (tpp) REVERT: G 37 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8117 (tm-30) REVERT: G 217 MET cc_start: 0.7839 (mmm) cc_final: 0.7422 (mmm) REVERT: G 279 TRP cc_start: 0.9147 (p-90) cc_final: 0.8615 (p-90) REVERT: G 327 GLU cc_start: 0.8070 (tt0) cc_final: 0.7644 (tt0) REVERT: G 347 ASP cc_start: 0.8225 (t0) cc_final: 0.7755 (t0) REVERT: G 393 ARG cc_start: 0.8249 (ttt90) cc_final: 0.7406 (tpp80) REVERT: H 28 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7559 (mm-40) REVERT: H 54 GLN cc_start: 0.7471 (tt0) cc_final: 0.7247 (tt0) REVERT: H 60 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7767 (ttm170) REVERT: H 67 ASN cc_start: 0.8488 (t0) cc_final: 0.8232 (t0) REVERT: H 73 LEU cc_start: 0.7332 (tp) cc_final: 0.6824 (mt) REVERT: H 97 VAL cc_start: 0.9236 (m) cc_final: 0.8940 (p) REVERT: H 99 LEU cc_start: 0.8880 (mp) cc_final: 0.8620 (mp) REVERT: H 104 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7009 (tm-30) REVERT: I 116 LEU cc_start: 0.9070 (tp) cc_final: 0.8719 (tp) REVERT: I 125 CYS cc_start: 0.8793 (t) cc_final: 0.8565 (t) REVERT: I 143 ASN cc_start: 0.8717 (t0) cc_final: 0.8495 (t0) REVERT: I 156 MET cc_start: 0.8303 (ppp) cc_final: 0.7942 (ppp) REVERT: I 160 GLU cc_start: 0.7965 (pm20) cc_final: 0.7587 (pm20) REVERT: I 164 VAL cc_start: 0.8859 (t) cc_final: 0.8636 (m) REVERT: I 193 TYR cc_start: 0.8632 (t80) cc_final: 0.7986 (t80) REVERT: I 198 PHE cc_start: 0.9032 (m-10) cc_final: 0.8578 (m-10) REVERT: I 214 ILE cc_start: 0.9077 (mp) cc_final: 0.8830 (pt) REVERT: I 222 VAL cc_start: 0.9058 (t) cc_final: 0.8800 (t) REVERT: I 243 ASN cc_start: 0.8234 (t0) cc_final: 0.7678 (m-40) REVERT: I 247 VAL cc_start: 0.9053 (t) cc_final: 0.8570 (t) REVERT: J 57 SER cc_start: 0.9144 (m) cc_final: 0.8415 (p) REVERT: J 251 LEU cc_start: 0.9329 (tp) cc_final: 0.9076 (tp) REVERT: J 257 PHE cc_start: 0.8821 (m-10) cc_final: 0.8608 (m-10) REVERT: J 366 ILE cc_start: 0.9425 (mt) cc_final: 0.9014 (tp) REVERT: J 390 GLU cc_start: 0.8745 (tt0) cc_final: 0.8205 (tm-30) REVERT: J 404 LYS cc_start: 0.9087 (mppt) cc_final: 0.8652 (tppt) REVERT: K 54 ASN cc_start: 0.7999 (p0) cc_final: 0.7708 (p0) REVERT: K 55 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8042 (tm-30) REVERT: K 97 LYS cc_start: 0.8856 (tptp) cc_final: 0.8606 (tptt) REVERT: K 142 PHE cc_start: 0.8364 (m-80) cc_final: 0.8095 (m-80) REVERT: K 156 ASP cc_start: 0.8526 (t0) cc_final: 0.8174 (t0) REVERT: K 158 LEU cc_start: 0.9307 (mt) cc_final: 0.8597 (mt) REVERT: K 305 ASP cc_start: 0.8564 (t0) cc_final: 0.8281 (t0) REVERT: K 330 TRP cc_start: 0.9353 (t-100) cc_final: 0.9019 (t-100) REVERT: K 334 GLU cc_start: 0.8604 (mp0) cc_final: 0.8347 (mp0) REVERT: K 347 ASP cc_start: 0.7655 (t70) cc_final: 0.7422 (t0) REVERT: K 354 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8410 (mt-10) REVERT: K 400 TYR cc_start: 0.8882 (m-80) cc_final: 0.8525 (m-80) REVERT: L 20 LEU cc_start: 0.7686 (mt) cc_final: 0.7181 (mp) REVERT: L 26 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8560 (tm-30) REVERT: L 27 GLU cc_start: 0.9021 (tp30) cc_final: 0.8773 (tp30) REVERT: L 28 GLN cc_start: 0.7749 (mm110) cc_final: 0.7102 (mm110) REVERT: L 43 LEU cc_start: 0.8859 (mt) cc_final: 0.8570 (mt) REVERT: L 77 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8365 (mm-30) REVERT: L 80 ASP cc_start: 0.8053 (t0) cc_final: 0.7637 (t0) REVERT: L 92 VAL cc_start: 0.8587 (t) cc_final: 0.8103 (t) REVERT: L 99 LEU cc_start: 0.9342 (mp) cc_final: 0.9096 (mt) REVERT: L 104 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6727 (tm-30) REVERT: L 106 PHE cc_start: 0.7589 (m-80) cc_final: 0.7150 (m-10) REVERT: L 109 GLU cc_start: 0.8547 (tt0) cc_final: 0.8235 (pm20) REVERT: L 111 GLU cc_start: 0.8692 (tt0) cc_final: 0.8426 (mm-30) REVERT: M 125 CYS cc_start: 0.7962 (t) cc_final: 0.7508 (t) REVERT: M 176 THR cc_start: 0.7434 (t) cc_final: 0.6756 (t) REVERT: M 178 ASP cc_start: 0.8530 (p0) cc_final: 0.8225 (p0) REVERT: M 195 ASN cc_start: 0.8873 (m-40) cc_final: 0.8586 (m110) REVERT: M 202 ARG cc_start: 0.8742 (ttp80) cc_final: 0.8080 (ttt90) REVERT: M 220 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8199 (mtm180) REVERT: N 187 TYR cc_start: 0.8911 (t80) cc_final: 0.8520 (t80) REVERT: N 321 LYS cc_start: 0.9188 (mtpp) cc_final: 0.8634 (mtpt) REVERT: N 396 GLN cc_start: 0.9216 (tt0) cc_final: 0.8941 (tt0) REVERT: O 34 VAL cc_start: 0.9612 (t) cc_final: 0.9302 (m) REVERT: O 67 MET cc_start: 0.8478 (tpp) cc_final: 0.8069 (tpp) REVERT: O 80 MET cc_start: 0.9357 (mmp) cc_final: 0.9070 (mmp) REVERT: O 125 THR cc_start: 0.9412 (m) cc_final: 0.8889 (p) REVERT: O 165 TYR cc_start: 0.8604 (p90) cc_final: 0.8158 (p90) REVERT: O 233 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7514 (tm-30) REVERT: P 80 ASP cc_start: 0.8465 (m-30) cc_final: 0.8209 (m-30) REVERT: P 104 GLU cc_start: 0.6949 (mp0) cc_final: 0.6716 (mp0) REVERT: Q 36 ASN cc_start: 0.8423 (t0) cc_final: 0.7821 (t0) REVERT: Q 55 THR cc_start: 0.8432 (p) cc_final: 0.8058 (t) REVERT: Q 77 GLU cc_start: 0.8351 (tp30) cc_final: 0.7681 (pt0) REVERT: Q 99 LEU cc_start: 0.9058 (mt) cc_final: 0.8814 (mt) REVERT: Q 104 GLU cc_start: 0.7213 (mp0) cc_final: 0.7008 (mp0) REVERT: R 115 MET cc_start: 0.8769 (mmm) cc_final: 0.8560 (mmp) REVERT: R 116 LEU cc_start: 0.9157 (tp) cc_final: 0.8902 (tp) REVERT: R 125 CYS cc_start: 0.9041 (t) cc_final: 0.8261 (t) REVERT: R 126 VAL cc_start: 0.9401 (m) cc_final: 0.9078 (m) REVERT: R 127 VAL cc_start: 0.9232 (t) cc_final: 0.9021 (m) REVERT: R 130 ARG cc_start: 0.8429 (ptp-110) cc_final: 0.8181 (ptm160) REVERT: R 133 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8414 (tmtt) REVERT: R 160 GLU cc_start: 0.8500 (mp0) cc_final: 0.7864 (mp0) REVERT: R 191 VAL cc_start: 0.8546 (m) cc_final: 0.8255 (p) REVERT: R 193 TYR cc_start: 0.8308 (t80) cc_final: 0.7947 (t80) REVERT: R 194 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7384 (tm-30) REVERT: R 197 ARG cc_start: 0.9269 (ttm-80) cc_final: 0.8806 (tpp-160) REVERT: R 202 ARG cc_start: 0.8754 (tpt-90) cc_final: 0.7513 (ttm-80) REVERT: R 207 LYS cc_start: 0.9389 (tttm) cc_final: 0.8980 (tptp) REVERT: R 209 ASP cc_start: 0.8287 (m-30) cc_final: 0.7826 (t0) REVERT: R 212 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8310 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 873 average time/residue: 0.4560 time to fit residues: 649.7948 Evaluate side-chains 735 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 735 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 282 optimal weight: 0.9990 chunk 269 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 252 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS G 71 HIS G 174 HIS G 249 HIS G 341 GLN ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 HIS J 399 GLN ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 GLN ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN R 143 ASN R 192 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.140753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104597 restraints weight = 73862.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108056 restraints weight = 36000.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109884 restraints weight = 19868.402| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34852 Z= 0.144 Angle : 0.653 15.597 47484 Z= 0.336 Chirality : 0.046 0.207 5340 Planarity : 0.005 0.062 6104 Dihedral : 5.056 30.670 4744 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.42 (0.13), residues: 4368 helix: 1.64 (0.24), residues: 502 sheet: -0.18 (0.13), residues: 1433 loop : -0.72 (0.13), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP M 186 HIS 0.011 0.001 HIS G 157 PHE 0.027 0.001 PHE P 98 TYR 0.026 0.001 TYR J 240 ARG 0.012 0.001 ARG O 303 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 1213) hydrogen bonds : angle 5.34144 ( 3426) SS BOND : bond 0.00366 ( 52) SS BOND : angle 1.67358 ( 104) covalent geometry : bond 0.00332 (34800) covalent geometry : angle 0.64877 (47380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 893 time to evaluate : 3.894 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8829 (mtm) cc_final: 0.8254 (mtp) REVERT: A 108 VAL cc_start: 0.9122 (m) cc_final: 0.8916 (p) REVERT: A 196 ASN cc_start: 0.9082 (m-40) cc_final: 0.8873 (m-40) REVERT: A 212 ASP cc_start: 0.8810 (p0) cc_final: 0.8391 (p0) REVERT: A 311 ASP cc_start: 0.8894 (p0) cc_final: 0.8573 (p0) REVERT: A 320 TYR cc_start: 0.8868 (p90) cc_final: 0.8305 (p90) REVERT: A 321 LYS cc_start: 0.9628 (mtpt) cc_final: 0.9406 (mtpp) REVERT: A 390 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8525 (pt0) REVERT: B 39 ASP cc_start: 0.8801 (m-30) cc_final: 0.8584 (m-30) REVERT: B 80 MET cc_start: 0.7620 (mmt) cc_final: 0.6742 (mmm) REVERT: B 156 ASP cc_start: 0.7897 (t0) cc_final: 0.7610 (t0) REVERT: B 239 ASN cc_start: 0.9054 (t0) cc_final: 0.8776 (t0) REVERT: E 125 CYS cc_start: 0.6920 (m) cc_final: 0.6532 (m) REVERT: E 140 LYS cc_start: 0.8615 (tptp) cc_final: 0.8336 (tptp) REVERT: E 186 TRP cc_start: 0.8066 (t60) cc_final: 0.7623 (t60) REVERT: E 197 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8554 (mtm110) REVERT: E 198 PHE cc_start: 0.8462 (m-80) cc_final: 0.8241 (m-10) REVERT: E 212 ARG cc_start: 0.7455 (mmm-85) cc_final: 0.7145 (mtt-85) REVERT: E 250 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8011 (ttmt) REVERT: F 43 ASN cc_start: 0.8913 (t0) cc_final: 0.8645 (t0) REVERT: F 66 LEU cc_start: 0.7645 (mt) cc_final: 0.7121 (mp) REVERT: F 99 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6890 (tm-30) REVERT: F 160 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8756 (tppt) REVERT: F 195 MET cc_start: 0.8928 (mpp) cc_final: 0.8189 (mpp) REVERT: F 218 ASP cc_start: 0.8516 (t0) cc_final: 0.8213 (t0) REVERT: F 320 TYR cc_start: 0.8032 (p90) cc_final: 0.7576 (p90) REVERT: F 340 LYS cc_start: 0.9394 (tttp) cc_final: 0.8912 (ttpp) REVERT: F 394 VAL cc_start: 0.9300 (t) cc_final: 0.8861 (p) REVERT: F 402 VAL cc_start: 0.8455 (t) cc_final: 0.8217 (t) REVERT: G 37 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8091 (tm-30) REVERT: G 168 MET cc_start: 0.8147 (mtp) cc_final: 0.7335 (mtp) REVERT: G 217 MET cc_start: 0.7883 (mmm) cc_final: 0.7508 (mmt) REVERT: G 279 TRP cc_start: 0.9178 (p-90) cc_final: 0.8680 (p-90) REVERT: G 280 PHE cc_start: 0.9085 (t80) cc_final: 0.8821 (t80) REVERT: G 327 GLU cc_start: 0.7882 (tt0) cc_final: 0.7448 (tt0) REVERT: G 347 ASP cc_start: 0.8341 (t0) cc_final: 0.7930 (t0) REVERT: G 360 TYR cc_start: 0.8737 (t80) cc_final: 0.7987 (t80) REVERT: G 393 ARG cc_start: 0.8236 (ttt90) cc_final: 0.7593 (tpp80) REVERT: H 28 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7599 (mm110) REVERT: H 54 GLN cc_start: 0.7524 (tt0) cc_final: 0.7286 (tt0) REVERT: H 67 ASN cc_start: 0.8527 (t0) cc_final: 0.8258 (t0) REVERT: H 97 VAL cc_start: 0.9192 (m) cc_final: 0.8857 (p) REVERT: H 104 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6921 (tm-30) REVERT: I 116 LEU cc_start: 0.9075 (tp) cc_final: 0.8718 (tp) REVERT: I 160 GLU cc_start: 0.7982 (pm20) cc_final: 0.7647 (pm20) REVERT: I 164 VAL cc_start: 0.8835 (t) cc_final: 0.8603 (m) REVERT: I 174 GLN cc_start: 0.8820 (mm110) cc_final: 0.8587 (mm110) REVERT: I 193 TYR cc_start: 0.8574 (t80) cc_final: 0.7828 (t80) REVERT: I 198 PHE cc_start: 0.8906 (m-10) cc_final: 0.8338 (m-10) REVERT: I 214 ILE cc_start: 0.9143 (mp) cc_final: 0.8914 (pt) REVERT: I 222 VAL cc_start: 0.9125 (t) cc_final: 0.8872 (t) REVERT: I 243 ASN cc_start: 0.8227 (t0) cc_final: 0.7710 (m-40) REVERT: I 247 VAL cc_start: 0.9014 (t) cc_final: 0.8559 (t) REVERT: J 57 SER cc_start: 0.9099 (m) cc_final: 0.8347 (p) REVERT: J 251 LEU cc_start: 0.9280 (tp) cc_final: 0.9068 (tp) REVERT: J 257 PHE cc_start: 0.8787 (m-10) cc_final: 0.8566 (m-10) REVERT: J 366 ILE cc_start: 0.9376 (mt) cc_final: 0.8988 (tp) REVERT: J 390 GLU cc_start: 0.8689 (tt0) cc_final: 0.8256 (tm-30) REVERT: J 399 GLN cc_start: 0.8366 (mm110) cc_final: 0.7772 (pp30) REVERT: J 404 LYS cc_start: 0.9044 (mppt) cc_final: 0.8642 (tppt) REVERT: K 54 ASN cc_start: 0.7907 (p0) cc_final: 0.7612 (p0) REVERT: K 97 LYS cc_start: 0.8611 (tptp) cc_final: 0.8337 (tptt) REVERT: K 156 ASP cc_start: 0.8415 (t0) cc_final: 0.8090 (t0) REVERT: K 158 LEU cc_start: 0.9263 (mt) cc_final: 0.8584 (mt) REVERT: K 305 ASP cc_start: 0.8513 (t0) cc_final: 0.8233 (t0) REVERT: K 330 TRP cc_start: 0.9271 (t-100) cc_final: 0.8870 (t-100) REVERT: K 334 GLU cc_start: 0.8607 (mp0) cc_final: 0.8372 (mp0) REVERT: K 351 TRP cc_start: 0.7520 (m100) cc_final: 0.7274 (m-10) REVERT: K 400 TYR cc_start: 0.8897 (m-80) cc_final: 0.8645 (m-80) REVERT: L 20 LEU cc_start: 0.7649 (mt) cc_final: 0.7172 (mp) REVERT: L 26 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8547 (tm-30) REVERT: L 27 GLU cc_start: 0.8968 (tp30) cc_final: 0.8690 (tp30) REVERT: L 28 GLN cc_start: 0.7661 (mm110) cc_final: 0.7015 (mm110) REVERT: L 43 LEU cc_start: 0.8816 (mt) cc_final: 0.8544 (mt) REVERT: L 77 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8511 (mm-30) REVERT: L 80 ASP cc_start: 0.8127 (t0) cc_final: 0.7625 (t0) REVERT: L 81 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7836 (tpm170) REVERT: L 92 VAL cc_start: 0.8532 (t) cc_final: 0.8147 (t) REVERT: L 101 ASN cc_start: 0.8934 (t0) cc_final: 0.7994 (m-40) REVERT: L 104 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6727 (tm-30) REVERT: L 106 PHE cc_start: 0.7514 (m-80) cc_final: 0.7157 (m-10) REVERT: L 109 GLU cc_start: 0.8637 (tt0) cc_final: 0.8282 (pm20) REVERT: L 111 GLU cc_start: 0.8612 (tt0) cc_final: 0.8397 (mm-30) REVERT: M 176 THR cc_start: 0.7200 (t) cc_final: 0.6406 (t) REVERT: M 194 GLU cc_start: 0.7621 (pp20) cc_final: 0.7025 (pp20) REVERT: M 202 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8097 (ttt90) REVERT: M 220 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8095 (mtm180) REVERT: N 66 LEU cc_start: 0.9129 (mt) cc_final: 0.8665 (mt) REVERT: N 143 ARG cc_start: 0.8480 (ttm110) cc_final: 0.7898 (ttm-80) REVERT: N 144 LEU cc_start: 0.8577 (mt) cc_final: 0.8285 (mt) REVERT: N 156 SER cc_start: 0.9029 (t) cc_final: 0.8817 (t) REVERT: N 187 TYR cc_start: 0.8835 (t80) cc_final: 0.8356 (t80) REVERT: N 284 ASP cc_start: 0.8828 (m-30) cc_final: 0.8534 (m-30) REVERT: N 321 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8909 (mtmm) REVERT: N 396 GLN cc_start: 0.9074 (tt0) cc_final: 0.8825 (tt0) REVERT: N 402 VAL cc_start: 0.9470 (t) cc_final: 0.9034 (p) REVERT: O 20 ARG cc_start: 0.8757 (tpt-90) cc_final: 0.8511 (tpt-90) REVERT: O 34 VAL cc_start: 0.9591 (t) cc_final: 0.9303 (m) REVERT: O 67 MET cc_start: 0.8386 (tpp) cc_final: 0.7917 (tpp) REVERT: O 80 MET cc_start: 0.9345 (mmp) cc_final: 0.9037 (mmt) REVERT: O 125 THR cc_start: 0.9348 (m) cc_final: 0.8845 (p) REVERT: O 165 TYR cc_start: 0.8581 (p90) cc_final: 0.8363 (p90) REVERT: P 80 ASP cc_start: 0.8618 (m-30) cc_final: 0.8398 (m-30) REVERT: P 96 GLU cc_start: 0.7469 (mp0) cc_final: 0.7265 (mp0) REVERT: P 104 GLU cc_start: 0.7231 (mp0) cc_final: 0.6980 (mp0) REVERT: Q 36 ASN cc_start: 0.8391 (t0) cc_final: 0.7752 (t0) REVERT: Q 77 GLU cc_start: 0.8224 (tp30) cc_final: 0.7731 (pt0) REVERT: Q 99 LEU cc_start: 0.9070 (mt) cc_final: 0.8803 (mt) REVERT: Q 104 GLU cc_start: 0.7374 (mp0) cc_final: 0.7040 (mp0) REVERT: R 115 MET cc_start: 0.8622 (mmm) cc_final: 0.8339 (mmm) REVERT: R 116 LEU cc_start: 0.9100 (tp) cc_final: 0.8711 (tp) REVERT: R 125 CYS cc_start: 0.8937 (t) cc_final: 0.8441 (t) REVERT: R 126 VAL cc_start: 0.9443 (m) cc_final: 0.9180 (m) REVERT: R 131 LEU cc_start: 0.9311 (tp) cc_final: 0.8900 (tp) REVERT: R 133 LYS cc_start: 0.8801 (tmmt) cc_final: 0.8491 (tmtt) REVERT: R 160 GLU cc_start: 0.8518 (mp0) cc_final: 0.7859 (mp0) REVERT: R 161 TYR cc_start: 0.9052 (p90) cc_final: 0.8654 (p90) REVERT: R 191 VAL cc_start: 0.8353 (m) cc_final: 0.8140 (t) REVERT: R 193 TYR cc_start: 0.8295 (t80) cc_final: 0.7899 (t80) REVERT: R 194 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7460 (tm-30) REVERT: R 197 ARG cc_start: 0.9320 (ttm-80) cc_final: 0.8898 (tpp-160) REVERT: R 207 LYS cc_start: 0.9369 (tttm) cc_final: 0.8995 (tptp) REVERT: R 209 ASP cc_start: 0.8304 (m-30) cc_final: 0.7847 (t0) REVERT: R 212 ARG cc_start: 0.8518 (tpp-160) cc_final: 0.8275 (tpp-160) REVERT: R 218 ARG cc_start: 0.7701 (ptt90) cc_final: 0.7044 (ptt90) outliers start: 0 outliers final: 0 residues processed: 893 average time/residue: 0.4418 time to fit residues: 642.5200 Evaluate side-chains 746 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 746 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 389 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 428 optimal weight: 4.9990 chunk 287 optimal weight: 7.9990 chunk 267 optimal weight: 0.0070 chunk 269 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 ASN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101741 restraints weight = 77096.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105794 restraints weight = 40301.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106857 restraints weight = 22007.664| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 34852 Z= 0.199 Angle : 0.665 15.413 47484 Z= 0.344 Chirality : 0.046 0.190 5340 Planarity : 0.005 0.078 6104 Dihedral : 5.070 30.696 4744 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.48 (0.13), residues: 4368 helix: 1.58 (0.24), residues: 502 sheet: -0.21 (0.13), residues: 1458 loop : -0.77 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP M 186 HIS 0.010 0.001 HIS A 392 PHE 0.027 0.002 PHE P 53 TYR 0.025 0.002 TYR O 99 ARG 0.013 0.001 ARG O 303 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 1213) hydrogen bonds : angle 5.33810 ( 3426) SS BOND : bond 0.00392 ( 52) SS BOND : angle 1.67866 ( 104) covalent geometry : bond 0.00454 (34800) covalent geometry : angle 0.66068 (47380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 859 time to evaluate : 3.980 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: 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 88 MET cc_start: 0.8834 (mtm) cc_final: 0.8289 (mtp) REVERT: A 212 ASP cc_start: 0.8807 (p0) cc_final: 0.8385 (p0) REVERT: A 311 ASP cc_start: 0.8886 (p0) cc_final: 0.8580 (p0) REVERT: A 320 TYR cc_start: 0.8874 (p90) cc_final: 0.8310 (p90) REVERT: A 321 LYS cc_start: 0.9651 (mtpt) cc_final: 0.9430 (mtpp) REVERT: A 390 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8524 (pt0) REVERT: B 39 ASP cc_start: 0.8808 (m-30) cc_final: 0.8593 (m-30) REVERT: B 80 MET cc_start: 0.7703 (mmt) cc_final: 0.6643 (mmm) REVERT: B 137 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8367 (mmm-85) REVERT: B 156 ASP cc_start: 0.7935 (t0) cc_final: 0.7710 (t0) REVERT: B 217 MET cc_start: 0.8562 (tpp) cc_final: 0.8306 (tpp) REVERT: B 239 ASN cc_start: 0.9077 (t0) cc_final: 0.8741 (t0) REVERT: B 294 LEU cc_start: 0.9011 (tp) cc_final: 0.8490 (tt) REVERT: E 114 ILE cc_start: 0.8745 (mm) cc_final: 0.8502 (mm) REVERT: E 125 CYS cc_start: 0.7023 (m) cc_final: 0.6584 (m) REVERT: E 141 ILE cc_start: 0.8624 (tp) cc_final: 0.8171 (tp) REVERT: E 153 LYS cc_start: 0.8372 (tmmt) cc_final: 0.7920 (tmmt) REVERT: E 185 ASN cc_start: 0.8944 (m-40) cc_final: 0.8741 (m-40) REVERT: E 186 TRP cc_start: 0.8194 (t60) cc_final: 0.7644 (t60) REVERT: E 194 GLU cc_start: 0.9012 (pp20) cc_final: 0.8647 (pp20) REVERT: E 216 ASP cc_start: 0.8804 (p0) cc_final: 0.8025 (p0) REVERT: E 218 ARG cc_start: 0.8796 (ptm160) cc_final: 0.8595 (ptm-80) REVERT: E 220 ARG cc_start: 0.8898 (mpp80) cc_final: 0.8296 (mtm-85) REVERT: E 250 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8259 (ttpp) REVERT: F 43 ASN cc_start: 0.8898 (t0) cc_final: 0.8632 (t0) REVERT: F 66 LEU cc_start: 0.7751 (mt) cc_final: 0.7231 (mp) REVERT: F 99 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6997 (tm-30) REVERT: F 143 ARG cc_start: 0.9093 (mmt-90) cc_final: 0.8869 (mpt180) REVERT: F 160 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8704 (tppt) REVERT: F 195 MET cc_start: 0.8911 (mpp) cc_final: 0.8336 (mpp) REVERT: F 218 ASP cc_start: 0.8520 (t0) cc_final: 0.8241 (t0) REVERT: F 320 TYR cc_start: 0.8014 (p90) cc_final: 0.7629 (p90) REVERT: F 340 LYS cc_start: 0.9313 (tttp) cc_final: 0.8816 (ttpp) REVERT: F 394 VAL cc_start: 0.9329 (t) cc_final: 0.8879 (p) REVERT: G 37 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8170 (tm-30) REVERT: G 217 MET cc_start: 0.7992 (mmm) cc_final: 0.7624 (mmt) REVERT: G 279 TRP cc_start: 0.9211 (p-90) cc_final: 0.8682 (p-90) REVERT: G 327 GLU cc_start: 0.7841 (tt0) cc_final: 0.7627 (tt0) REVERT: G 347 ASP cc_start: 0.8331 (t0) cc_final: 0.7852 (t0) REVERT: G 360 TYR cc_start: 0.8707 (t80) cc_final: 0.7988 (t80) REVERT: G 393 ARG cc_start: 0.8174 (ttt90) cc_final: 0.7346 (tpp80) REVERT: H 28 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7540 (mm110) REVERT: H 67 ASN cc_start: 0.8538 (t0) cc_final: 0.8271 (t0) REVERT: H 97 VAL cc_start: 0.9211 (m) cc_final: 0.8877 (p) REVERT: H 99 LEU cc_start: 0.8977 (mt) cc_final: 0.8617 (mt) REVERT: H 104 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6957 (tm-30) REVERT: H 111 GLU cc_start: 0.3724 (tp30) cc_final: 0.3226 (tp30) REVERT: I 153 LYS cc_start: 0.8970 (mppt) cc_final: 0.8684 (mppt) REVERT: I 156 MET cc_start: 0.8610 (ppp) cc_final: 0.7984 (ttp) REVERT: I 157 TYR cc_start: 0.8061 (m-80) cc_final: 0.7738 (m-80) REVERT: I 160 GLU cc_start: 0.7964 (pm20) cc_final: 0.7611 (mp0) REVERT: I 164 VAL cc_start: 0.8815 (t) cc_final: 0.8614 (m) REVERT: I 193 TYR cc_start: 0.8510 (t80) cc_final: 0.7804 (t80) REVERT: I 198 PHE cc_start: 0.8996 (m-10) cc_final: 0.8469 (m-10) REVERT: I 214 ILE cc_start: 0.9100 (mp) cc_final: 0.8853 (pt) REVERT: I 222 VAL cc_start: 0.9133 (t) cc_final: 0.8909 (t) REVERT: I 243 ASN cc_start: 0.8220 (t0) cc_final: 0.7691 (m-40) REVERT: I 247 VAL cc_start: 0.9094 (t) cc_final: 0.8851 (t) REVERT: I 249 ILE cc_start: 0.8452 (mt) cc_final: 0.8186 (tp) REVERT: J 57 SER cc_start: 0.9129 (m) cc_final: 0.8464 (p) REVERT: J 251 LEU cc_start: 0.9311 (tp) cc_final: 0.9076 (tp) REVERT: J 257 PHE cc_start: 0.8794 (m-10) cc_final: 0.8556 (m-10) REVERT: J 366 ILE cc_start: 0.9399 (mt) cc_final: 0.9026 (tp) REVERT: J 390 GLU cc_start: 0.8653 (tt0) cc_final: 0.8215 (tm-30) REVERT: J 404 LYS cc_start: 0.9028 (mppt) cc_final: 0.8610 (tppt) REVERT: J 439 ARG cc_start: 0.6303 (ttp80) cc_final: 0.6055 (ptt180) REVERT: K 54 ASN cc_start: 0.7898 (p0) cc_final: 0.7621 (p0) REVERT: K 97 LYS cc_start: 0.8714 (tptp) cc_final: 0.8434 (tptt) REVERT: K 158 LEU cc_start: 0.9246 (mt) cc_final: 0.8559 (mt) REVERT: K 233 GLN cc_start: 0.8972 (pm20) cc_final: 0.8761 (pm20) REVERT: K 305 ASP cc_start: 0.8545 (t0) cc_final: 0.8227 (t0) REVERT: K 309 GLU cc_start: 0.8014 (tt0) cc_final: 0.7721 (tt0) REVERT: K 330 TRP cc_start: 0.9306 (t-100) cc_final: 0.8942 (t-100) REVERT: K 400 TYR cc_start: 0.8861 (m-80) cc_final: 0.8555 (m-80) REVERT: L 20 LEU cc_start: 0.7647 (mt) cc_final: 0.7140 (mp) REVERT: L 26 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8795 (tp30) REVERT: L 27 GLU cc_start: 0.8982 (tp30) cc_final: 0.8623 (tp30) REVERT: L 28 GLN cc_start: 0.7761 (mm110) cc_final: 0.7209 (mm110) REVERT: L 43 LEU cc_start: 0.8915 (mt) cc_final: 0.8584 (mt) REVERT: L 69 GLU cc_start: 0.9029 (mp0) cc_final: 0.8756 (mp0) REVERT: L 77 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8389 (mm-30) REVERT: L 79 ILE cc_start: 0.8380 (mm) cc_final: 0.8148 (mm) REVERT: L 92 VAL cc_start: 0.8566 (t) cc_final: 0.8120 (t) REVERT: L 99 LEU cc_start: 0.9183 (mt) cc_final: 0.8954 (mt) REVERT: L 103 LEU cc_start: 0.7922 (tp) cc_final: 0.7694 (tp) REVERT: L 104 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6678 (tm-30) REVERT: L 106 PHE cc_start: 0.7461 (m-80) cc_final: 0.7135 (m-10) REVERT: L 109 GLU cc_start: 0.8630 (tt0) cc_final: 0.8309 (pm20) REVERT: L 111 GLU cc_start: 0.8680 (tt0) cc_final: 0.8433 (mm-30) REVERT: M 125 CYS cc_start: 0.8016 (t) cc_final: 0.7796 (t) REVERT: M 163 ASP cc_start: 0.8293 (t0) cc_final: 0.8069 (t0) REVERT: M 176 THR cc_start: 0.7412 (t) cc_final: 0.6100 (t) REVERT: M 178 ASP cc_start: 0.8439 (p0) cc_final: 0.8133 (p0) REVERT: M 202 ARG cc_start: 0.8727 (ttp80) cc_final: 0.8377 (ttt90) REVERT: M 220 ARG cc_start: 0.8624 (mtm180) cc_final: 0.8131 (mtm180) REVERT: N 66 LEU cc_start: 0.9154 (mt) cc_final: 0.8753 (mt) REVERT: N 143 ARG cc_start: 0.8492 (ttm110) cc_final: 0.7907 (ttm-80) REVERT: N 144 LEU cc_start: 0.8553 (mt) cc_final: 0.8274 (mt) REVERT: N 187 TYR cc_start: 0.8837 (t80) cc_final: 0.8380 (t80) REVERT: N 284 ASP cc_start: 0.8860 (m-30) cc_final: 0.8546 (m-30) REVERT: N 321 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8761 (mtmm) REVERT: N 396 GLN cc_start: 0.9083 (tt0) cc_final: 0.8824 (tt0) REVERT: N 402 VAL cc_start: 0.9464 (t) cc_final: 0.8986 (p) REVERT: O 20 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.8225 (tpt90) REVERT: O 29 ILE cc_start: 0.9214 (pt) cc_final: 0.8992 (pt) REVERT: O 34 VAL cc_start: 0.9595 (t) cc_final: 0.9308 (m) REVERT: O 67 MET cc_start: 0.8398 (tpp) cc_final: 0.7931 (tpp) REVERT: O 80 MET cc_start: 0.9314 (mmp) cc_final: 0.8881 (tpp) REVERT: O 125 THR cc_start: 0.9390 (m) cc_final: 0.8881 (p) REVERT: O 165 TYR cc_start: 0.8558 (p90) cc_final: 0.8334 (p90) REVERT: P 80 ASP cc_start: 0.8627 (m-30) cc_final: 0.8245 (m-30) REVERT: P 96 GLU cc_start: 0.7386 (mp0) cc_final: 0.7181 (mp0) REVERT: P 104 GLU cc_start: 0.7165 (mp0) cc_final: 0.6929 (mp0) REVERT: Q 54 GLN cc_start: 0.8458 (tt0) cc_final: 0.8248 (tt0) REVERT: Q 55 THR cc_start: 0.8453 (p) cc_final: 0.8081 (t) REVERT: Q 77 GLU cc_start: 0.8308 (tp30) cc_final: 0.7663 (pt0) REVERT: Q 99 LEU cc_start: 0.9042 (mt) cc_final: 0.8811 (mt) REVERT: Q 104 GLU cc_start: 0.7255 (mp0) cc_final: 0.6828 (mp0) REVERT: R 115 MET cc_start: 0.8656 (mmm) cc_final: 0.8331 (mmm) REVERT: R 125 CYS cc_start: 0.9015 (t) cc_final: 0.8473 (t) REVERT: R 126 VAL cc_start: 0.9372 (m) cc_final: 0.9111 (m) REVERT: R 133 LYS cc_start: 0.8761 (tmmt) cc_final: 0.8450 (tmtt) REVERT: R 143 ASN cc_start: 0.6409 (m-40) cc_final: 0.6094 (t0) REVERT: R 160 GLU cc_start: 0.8701 (mp0) cc_final: 0.8060 (mp0) REVERT: R 191 VAL cc_start: 0.8422 (m) cc_final: 0.8149 (t) REVERT: R 193 TYR cc_start: 0.8385 (t80) cc_final: 0.7959 (t80) REVERT: R 194 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7531 (tm-30) REVERT: R 197 ARG cc_start: 0.9303 (ttm-80) cc_final: 0.8885 (tpp-160) REVERT: R 207 LYS cc_start: 0.9396 (tttm) cc_final: 0.8992 (tptp) REVERT: R 209 ASP cc_start: 0.8275 (m-30) cc_final: 0.7841 (t0) REVERT: R 212 ARG cc_start: 0.8513 (tpp-160) cc_final: 0.8252 (tpp-160) REVERT: R 220 ARG cc_start: 0.8534 (mtp-110) cc_final: 0.8321 (mtm110) REVERT: R 250 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7309 (mttt) outliers start: 1 outliers final: 0 residues processed: 860 average time/residue: 0.4669 time to fit residues: 650.7113 Evaluate side-chains 745 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 320 optimal weight: 0.0020 chunk 137 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 286 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 127 optimal weight: 40.0000 chunk 361 optimal weight: 0.5980 chunk 415 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 overall best weight: 3.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS E 195 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS G 174 HIS G 341 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102930 restraints weight = 76903.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107440 restraints weight = 39366.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108133 restraints weight = 20876.663| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34852 Z= 0.168 Angle : 0.661 16.407 47484 Z= 0.340 Chirality : 0.046 0.187 5340 Planarity : 0.005 0.075 6104 Dihedral : 5.050 28.326 4744 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.49 (0.13), residues: 4368 helix: 1.61 (0.24), residues: 491 sheet: -0.31 (0.13), residues: 1467 loop : -0.70 (0.13), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP M 186 HIS 0.008 0.001 HIS A 392 PHE 0.028 0.002 PHE P 53 TYR 0.022 0.001 TYR O 99 ARG 0.015 0.001 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1213) hydrogen bonds : angle 5.29973 ( 3426) SS BOND : bond 0.00376 ( 52) SS BOND : angle 1.55347 ( 104) covalent geometry : bond 0.00388 (34800) covalent geometry : angle 0.65733 (47380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 873 time to evaluate : 3.477 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: 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 88 MET cc_start: 0.8826 (mtm) cc_final: 0.8259 (mtp) REVERT: A 212 ASP cc_start: 0.8779 (p0) cc_final: 0.8368 (p0) REVERT: A 311 ASP cc_start: 0.8803 (p0) cc_final: 0.8497 (p0) REVERT: A 320 TYR cc_start: 0.8870 (p90) cc_final: 0.8319 (p90) REVERT: A 321 LYS cc_start: 0.9616 (mtpt) cc_final: 0.9396 (mtpp) REVERT: B 39 ASP cc_start: 0.8771 (m-30) cc_final: 0.8549 (m-30) REVERT: B 80 MET cc_start: 0.7673 (mmt) cc_final: 0.6590 (mmm) REVERT: B 156 ASP cc_start: 0.7968 (t0) cc_final: 0.7687 (t0) REVERT: B 217 MET cc_start: 0.8573 (tpp) cc_final: 0.8313 (tpp) REVERT: B 239 ASN cc_start: 0.9056 (t0) cc_final: 0.8744 (t0) REVERT: B 294 LEU cc_start: 0.8970 (tp) cc_final: 0.8584 (tt) REVERT: E 125 CYS cc_start: 0.7053 (m) cc_final: 0.6641 (m) REVERT: E 140 LYS cc_start: 0.8527 (tptt) cc_final: 0.8046 (tptt) REVERT: E 153 LYS cc_start: 0.8337 (tmmt) cc_final: 0.8105 (tmmt) REVERT: E 185 ASN cc_start: 0.8963 (m-40) cc_final: 0.8746 (m-40) REVERT: E 186 TRP cc_start: 0.8132 (t60) cc_final: 0.7756 (t60) REVERT: E 188 HIS cc_start: 0.9052 (m-70) cc_final: 0.8765 (m-70) REVERT: E 194 GLU cc_start: 0.8744 (pp20) cc_final: 0.8134 (pp20) REVERT: E 216 ASP cc_start: 0.8831 (p0) cc_final: 0.8493 (p0) REVERT: E 250 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8302 (ttpp) REVERT: F 43 ASN cc_start: 0.8904 (t0) cc_final: 0.8627 (t0) REVERT: F 66 LEU cc_start: 0.7685 (mt) cc_final: 0.7131 (mp) REVERT: F 99 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6903 (tm-30) REVERT: F 160 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8716 (tppt) REVERT: F 195 MET cc_start: 0.8919 (mpp) cc_final: 0.8192 (mpp) REVERT: F 218 ASP cc_start: 0.8508 (t0) cc_final: 0.8220 (t0) REVERT: F 320 TYR cc_start: 0.7952 (p90) cc_final: 0.7594 (p90) REVERT: F 340 LYS cc_start: 0.9362 (tttp) cc_final: 0.8863 (ttpp) REVERT: F 394 VAL cc_start: 0.9332 (t) cc_final: 0.8896 (p) REVERT: G 37 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8130 (tm-30) REVERT: G 67 MET cc_start: 0.8782 (tpt) cc_final: 0.8463 (tpp) REVERT: G 217 MET cc_start: 0.8028 (mmm) cc_final: 0.7605 (mmm) REVERT: G 279 TRP cc_start: 0.9185 (p-90) cc_final: 0.8667 (p-90) REVERT: G 327 GLU cc_start: 0.7857 (tt0) cc_final: 0.7593 (tt0) REVERT: G 347 ASP cc_start: 0.8354 (t0) cc_final: 0.7874 (t0) REVERT: G 351 TRP cc_start: 0.9002 (m100) cc_final: 0.8740 (m100) REVERT: G 393 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7253 (tpp80) REVERT: G 396 CYS cc_start: 0.8717 (m) cc_final: 0.8321 (p) REVERT: H 21 HIS cc_start: 0.6186 (t70) cc_final: 0.5694 (t70) REVERT: H 28 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7465 (mm110) REVERT: H 67 ASN cc_start: 0.8491 (t0) cc_final: 0.8259 (t0) REVERT: H 97 VAL cc_start: 0.9163 (m) cc_final: 0.8826 (p) REVERT: H 104 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6971 (tm-30) REVERT: I 153 LYS cc_start: 0.9026 (mppt) cc_final: 0.8763 (mppt) REVERT: I 156 MET cc_start: 0.8578 (ppp) cc_final: 0.8075 (ttt) REVERT: I 160 GLU cc_start: 0.7999 (pm20) cc_final: 0.7610 (mp0) REVERT: I 193 TYR cc_start: 0.8553 (t80) cc_final: 0.7802 (t80) REVERT: I 198 PHE cc_start: 0.8960 (m-10) cc_final: 0.8436 (m-10) REVERT: I 214 ILE cc_start: 0.9092 (mp) cc_final: 0.8853 (pt) REVERT: I 222 VAL cc_start: 0.9110 (t) cc_final: 0.8887 (t) REVERT: I 243 ASN cc_start: 0.8207 (t0) cc_final: 0.7708 (m-40) REVERT: I 249 ILE cc_start: 0.8453 (mt) cc_final: 0.8226 (tp) REVERT: J 57 SER cc_start: 0.9078 (m) cc_final: 0.8385 (p) REVERT: J 251 LEU cc_start: 0.9309 (tp) cc_final: 0.9082 (tp) REVERT: J 257 PHE cc_start: 0.8783 (m-10) cc_final: 0.8495 (m-10) REVERT: J 366 ILE cc_start: 0.9398 (mt) cc_final: 0.9024 (tp) REVERT: J 390 GLU cc_start: 0.8662 (tt0) cc_final: 0.8305 (tm-30) REVERT: J 399 GLN cc_start: 0.8329 (mm110) cc_final: 0.7820 (pp30) REVERT: J 404 LYS cc_start: 0.9024 (mppt) cc_final: 0.8618 (tppt) REVERT: J 439 ARG cc_start: 0.6380 (ttp80) cc_final: 0.6013 (ptt-90) REVERT: K 97 LYS cc_start: 0.8620 (tptp) cc_final: 0.8332 (tptt) REVERT: K 156 ASP cc_start: 0.8444 (t0) cc_final: 0.8165 (t0) REVERT: K 158 LEU cc_start: 0.9159 (mt) cc_final: 0.8569 (mt) REVERT: K 235 LYS cc_start: 0.3777 (tptt) cc_final: 0.3373 (tptt) REVERT: K 305 ASP cc_start: 0.8535 (t0) cc_final: 0.8206 (t0) REVERT: K 330 TRP cc_start: 0.9302 (t-100) cc_final: 0.8911 (t-100) REVERT: K 351 TRP cc_start: 0.7549 (m100) cc_final: 0.7293 (m-10) REVERT: K 400 TYR cc_start: 0.8855 (m-80) cc_final: 0.8574 (m-80) REVERT: L 20 LEU cc_start: 0.7726 (mt) cc_final: 0.7211 (mp) REVERT: L 26 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8711 (tm-30) REVERT: L 28 GLN cc_start: 0.7785 (mm110) cc_final: 0.7021 (mm110) REVERT: L 43 LEU cc_start: 0.8973 (mt) cc_final: 0.8657 (mt) REVERT: L 77 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8532 (mm-30) REVERT: L 80 ASP cc_start: 0.7797 (t0) cc_final: 0.7454 (t0) REVERT: L 92 VAL cc_start: 0.8614 (t) cc_final: 0.8160 (t) REVERT: L 99 LEU cc_start: 0.9200 (mt) cc_final: 0.8967 (mt) REVERT: L 104 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6709 (tm-30) REVERT: L 106 PHE cc_start: 0.7424 (m-80) cc_final: 0.7143 (m-10) REVERT: L 109 GLU cc_start: 0.8625 (tt0) cc_final: 0.8308 (pm20) REVERT: M 125 CYS cc_start: 0.8020 (t) cc_final: 0.7817 (t) REVERT: M 163 ASP cc_start: 0.8300 (t0) cc_final: 0.8067 (t0) REVERT: M 176 THR cc_start: 0.7370 (t) cc_final: 0.6527 (t) REVERT: M 194 GLU cc_start: 0.7711 (pp20) cc_final: 0.7187 (pp20) REVERT: M 197 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7917 (mmm160) REVERT: M 202 ARG cc_start: 0.8680 (ttp80) cc_final: 0.7983 (ttt90) REVERT: M 212 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8083 (mmm-85) REVERT: M 220 ARG cc_start: 0.8713 (mtm180) cc_final: 0.8197 (mtm180) REVERT: M 244 GLN cc_start: 0.9161 (pm20) cc_final: 0.8942 (pp30) REVERT: N 144 LEU cc_start: 0.8601 (mt) cc_final: 0.8334 (mt) REVERT: N 187 TYR cc_start: 0.8785 (t80) cc_final: 0.8285 (t80) REVERT: N 321 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8780 (mtmm) REVERT: N 396 GLN cc_start: 0.9073 (tt0) cc_final: 0.8822 (tt0) REVERT: N 402 VAL cc_start: 0.9375 (t) cc_final: 0.9072 (p) REVERT: O 20 ARG cc_start: 0.8437 (tpt-90) cc_final: 0.8150 (tpt90) REVERT: O 34 VAL cc_start: 0.9599 (t) cc_final: 0.9329 (m) REVERT: O 67 MET cc_start: 0.8469 (tpp) cc_final: 0.7945 (tpp) REVERT: O 80 MET cc_start: 0.9373 (mmp) cc_final: 0.8943 (mmt) REVERT: O 125 THR cc_start: 0.9384 (m) cc_final: 0.8877 (p) REVERT: O 165 TYR cc_start: 0.8521 (p90) cc_final: 0.8284 (p90) REVERT: P 55 THR cc_start: 0.8954 (p) cc_final: 0.8628 (p) REVERT: P 80 ASP cc_start: 0.8614 (m-30) cc_final: 0.8389 (m-30) REVERT: P 93 LEU cc_start: 0.8580 (mt) cc_final: 0.8327 (mt) REVERT: P 104 GLU cc_start: 0.7172 (mp0) cc_final: 0.6949 (mp0) REVERT: Q 55 THR cc_start: 0.8436 (p) cc_final: 0.8129 (t) REVERT: Q 77 GLU cc_start: 0.8307 (tp30) cc_final: 0.7704 (pt0) REVERT: Q 99 LEU cc_start: 0.9090 (mt) cc_final: 0.8788 (mt) REVERT: Q 104 GLU cc_start: 0.7320 (mp0) cc_final: 0.6988 (mp0) REVERT: R 115 MET cc_start: 0.8618 (mmm) cc_final: 0.8366 (mmm) REVERT: R 125 CYS cc_start: 0.9019 (t) cc_final: 0.8501 (t) REVERT: R 126 VAL cc_start: 0.9322 (m) cc_final: 0.9083 (m) REVERT: R 133 LYS cc_start: 0.8846 (tmmt) cc_final: 0.8638 (tmtt) REVERT: R 160 GLU cc_start: 0.8640 (mp0) cc_final: 0.8017 (mp0) REVERT: R 193 TYR cc_start: 0.8438 (t80) cc_final: 0.7954 (t80) REVERT: R 194 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7165 (tm-30) REVERT: R 197 ARG cc_start: 0.9286 (ttm-80) cc_final: 0.8902 (tpp-160) REVERT: R 207 LYS cc_start: 0.9391 (tttm) cc_final: 0.9005 (tptp) REVERT: R 209 ASP cc_start: 0.8276 (m-30) cc_final: 0.7853 (t0) REVERT: R 212 ARG cc_start: 0.8503 (tpp-160) cc_final: 0.8276 (tpp-160) REVERT: R 250 LYS cc_start: 0.7678 (ttmm) cc_final: 0.7339 (mttt) outliers start: 1 outliers final: 0 residues processed: 874 average time/residue: 0.4435 time to fit residues: 629.6939 Evaluate side-chains 745 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 348 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 393 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 127 optimal weight: 40.0000 chunk 329 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 396 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS G 174 HIS ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 ASN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 HIS ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN R 143 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103283 restraints weight = 77299.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107595 restraints weight = 39197.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108442 restraints weight = 21479.298| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34852 Z= 0.158 Angle : 0.656 16.601 47484 Z= 0.338 Chirality : 0.046 0.236 5340 Planarity : 0.005 0.067 6104 Dihedral : 5.048 27.662 4744 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.44 (0.13), residues: 4368 helix: 1.57 (0.24), residues: 505 sheet: -0.23 (0.13), residues: 1467 loop : -0.69 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP M 186 HIS 0.007 0.001 HIS A 392 PHE 0.028 0.001 PHE P 53 TYR 0.019 0.001 TYR O 99 ARG 0.013 0.001 ARG O 303 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 1213) hydrogen bonds : angle 5.25344 ( 3426) SS BOND : bond 0.00352 ( 52) SS BOND : angle 1.57911 ( 104) covalent geometry : bond 0.00365 (34800) covalent geometry : angle 0.65259 (47380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15163.69 seconds wall clock time: 264 minutes 3.66 seconds (15843.66 seconds total)