Starting phenix.real_space_refine on Sun Jun 22 20:36:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fd2_29000/06_2025/8fd2_29000.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd2_29000/06_2025/8fd2_29000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fd2_29000/06_2025/8fd2_29000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd2_29000/06_2025/8fd2_29000.map" model { file = "/net/cci-nas-00/data/ceres_data/8fd2_29000/06_2025/8fd2_29000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd2_29000/06_2025/8fd2_29000.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 408 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 94 5.16 5 C 16320 2.51 5 N 4376 2.21 5 O 4944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 1.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25797 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1727 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2345 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2351 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 20} Link IDs: {'rna2p': 25, 'rna3p': 37} Time building chain proxies: 15.39, per 1000 atoms: 0.60 Number of scatterers: 25797 At special positions: 0 Unit cell: (102.238, 119.102, 196.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 63 15.00 O 4944 8.00 N 4376 7.00 C 16320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.44 Conformation dependent library (CDL) restraints added in 2.8 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5590 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 51 sheets defined 39.4% alpha, 23.4% beta 2 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 9.53 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.584A pdb=" N TRP A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.325A pdb=" N GLU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.817A pdb=" N MET B 204 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.618A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.730A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.573A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.645A pdb=" N SER C 214 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.552A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.662A pdb=" N ASP C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.577A pdb=" N ILE D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.522A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.784A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.084A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.598A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.522A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.883A pdb=" N GLY E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 284 removed outlier: 4.093A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.644A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.773A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.826A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.956A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 71 removed outlier: 3.747A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.644A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 4.009A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 318 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.531A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 109 through 112 Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.573A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.679A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 285 removed outlier: 3.920A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.603A pdb=" N LYS H 295 " --> pdb=" O PRO H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 317 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.747A pdb=" N ILE I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.585A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 116 through 118 No H-bonds generated for 'chain 'I' and resid 116 through 118' Processing helix chain 'I' and resid 148 through 157 removed outlier: 5.400A pdb=" N ALA I 153 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 removed outlier: 3.505A pdb=" N GLN I 187 " --> pdb=" O ALA I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 251 through 252 No H-bonds generated for 'chain 'I' and resid 251 through 252' Processing helix chain 'I' and resid 253 through 256 Processing helix chain 'I' and resid 261 through 270 removed outlier: 3.538A pdb=" N TYR I 270 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 Processing helix chain 'I' and resid 361 through 367 removed outlier: 3.667A pdb=" N LYS I 365 " --> pdb=" O ASN I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 382 removed outlier: 4.030A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU I 379 " --> pdb=" O LEU I 375 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE I 380 " --> pdb=" O PHE I 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 381 " --> pdb=" O ASN I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 392 Processing helix chain 'I' and resid 397 through 421 removed outlier: 3.686A pdb=" N ILE I 417 " --> pdb=" O ASN I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 removed outlier: 3.835A pdb=" N LYS I 432 " --> pdb=" O PRO I 428 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS I 443 " --> pdb=" O GLU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 460 Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 6 through 33 Processing helix chain 'J' and resid 41 through 53 Processing helix chain 'J' and resid 58 through 72 removed outlier: 5.965A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.716A pdb=" N ILE J 85 " --> pdb=" O HIS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 107 Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.525A pdb=" N LYS J 111 " --> pdb=" O TYR J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.816A pdb=" N VAL K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.605A pdb=" N GLY K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 93 through 107 Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.769A pdb=" N CYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.806A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 Processing helix chain 'L' and resid 81 through 92 Processing helix chain 'L' and resid 93 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.914A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.523A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.589A pdb=" N PHE A 13 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER A 97 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.026A pdb=" N ARG B 19 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 100 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.358A pdb=" N LEU B 109 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N GLU B 10 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N LYS B 107 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N VAL B 12 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ASP B 105 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 5.582A pdb=" N VAL B 179 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG B 118 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 181 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR B 116 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.658A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.658A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR C 180 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 15 " --> pdb=" O TRP C 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP C 230 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 17 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE C 228 " --> pdb=" O TYR C 17 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 19 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 226 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 21 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.662A pdb=" N GLY C 25 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.546A pdb=" N SER C 169 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR D 180 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.541A pdb=" N GLY D 25 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.996A pdb=" N THR D 39 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 244 Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AC9, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AD1, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 25 through 26 removed outlier: 3.512A pdb=" N GLY F 25 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 178 " --> pdb=" O GLY F 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.531A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD6, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.521A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.521A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY G 276 " --> pdb=" O TYR G 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE1, first strand: chain 'G' and resid 77 through 80 removed outlier: 3.633A pdb=" N ILE G 85 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 106 through 107 removed outlier: 3.673A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE4, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AE8, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE9, first strand: chain 'H' and resid 105 through 107 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.570A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AF3, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.476A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.255A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 329 through 333 1109 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 12.87 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7226 1.33 - 1.45: 5111 1.45 - 1.57: 13951 1.57 - 1.69: 125 1.69 - 1.81: 149 Bond restraints: 26562 Sorted by residual: bond pdb=" CA SER F 28 " pdb=" C SER F 28 " ideal model delta sigma weight residual 1.532 1.507 0.026 1.21e-02 6.83e+03 4.52e+00 bond pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.61e-02 3.86e+03 2.33e+00 bond pdb=" CA LYS G 250 " pdb=" CB LYS G 250 " ideal model delta sigma weight residual 1.526 1.553 -0.026 1.76e-02 3.23e+03 2.26e+00 bond pdb=" O5' U M 34 " pdb=" C5' U M 34 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.85e+00 bond pdb=" C3' G M 48 " pdb=" O3' G M 48 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.78e+00 ... (remaining 26557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 35794 2.36 - 4.72: 330 4.72 - 7.07: 39 7.07 - 9.43: 7 9.43 - 11.79: 2 Bond angle restraints: 36172 Sorted by residual: angle pdb=" N SER E 28 " pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 110.44 103.37 7.07 1.20e+00 6.94e-01 3.47e+01 angle pdb=" N LEU E 29 " pdb=" CA LEU E 29 " pdb=" C LEU E 29 " ideal model delta sigma weight residual 111.03 117.40 -6.37 1.11e+00 8.12e-01 3.30e+01 angle pdb=" N TYR H 244 " pdb=" CA TYR H 244 " pdb=" C TYR H 244 " ideal model delta sigma weight residual 114.56 108.29 6.27 1.27e+00 6.20e-01 2.44e+01 angle pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta sigma weight residual 117.23 111.01 6.22 1.36e+00 5.41e-01 2.09e+01 angle pdb=" N SER I 260 " pdb=" CA SER I 260 " pdb=" C SER I 260 " ideal model delta sigma weight residual 113.61 107.25 6.36 1.50e+00 4.44e-01 1.80e+01 ... (remaining 36167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 15226 35.83 - 71.67: 643 71.67 - 107.50: 42 107.50 - 143.34: 1 143.34 - 179.17: 5 Dihedral angle restraints: 15917 sinusoidal: 7192 harmonic: 8725 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 44.58 155.42 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 73.30 126.70 1 1.50e+01 4.44e-03 6.82e+01 dihedral pdb=" O4' C M 50 " pdb=" C1' C M 50 " pdb=" N1 C M 50 " pdb=" C2 C M 50 " ideal model delta sinusoidal sigma weight residual -128.00 51.17 -179.17 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2770 0.036 - 0.072: 774 0.072 - 0.108: 250 0.108 - 0.145: 64 0.145 - 0.181: 11 Chirality restraints: 3869 Sorted by residual: chirality pdb=" CA PRO F 247 " pdb=" N PRO F 247 " pdb=" C PRO F 247 " pdb=" CB PRO F 247 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA TYR I 334 " pdb=" N TYR I 334 " pdb=" C TYR I 334 " pdb=" CB TYR I 334 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" C1' U M 20 " pdb=" O4' U M 20 " pdb=" C2' U M 20 " pdb=" N1 U M 20 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 3866 not shown) Planarity restraints: 4399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C PHE J 61 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.060 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO F 247 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " -0.042 5.00e-02 4.00e+02 6.46e-02 6.69e+00 pdb=" N PRO B 210 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.036 5.00e-02 4.00e+02 ... (remaining 4396 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 785 2.69 - 3.24: 24850 3.24 - 3.79: 42277 3.79 - 4.35: 58691 4.35 - 4.90: 95244 Nonbonded interactions: 221847 Sorted by model distance: nonbonded pdb=" O LEU B 184 " pdb=" ND2 ASN B 185 " model vdw 2.136 3.120 nonbonded pdb=" N GLU G 257 " pdb=" OE1 GLU G 257 " model vdw 2.194 3.120 nonbonded pdb=" OG1 THR A 15 " pdb=" NE2 GLN A 143 " model vdw 2.202 3.120 nonbonded pdb=" N GLU J 83 " pdb=" OE1 GLU J 83 " model vdw 2.206 3.120 nonbonded pdb=" OG1 THR E 19 " pdb=" O SER E 239 " model vdw 2.220 3.040 ... (remaining 221842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = (chain 'G' and (resid 12 through 109 or resid 133 through 319)) selection = (chain 'H' and (resid 12 through 109 or resid 133 through 319)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 68.220 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26562 Z= 0.131 Angle : 0.572 11.789 36172 Z= 0.309 Chirality : 0.040 0.181 3869 Planarity : 0.004 0.092 4399 Dihedral : 17.940 179.170 10327 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.40 % Favored : 94.26 % Rotamer: Outliers : 2.84 % Allowed : 20.68 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.16), residues: 2943 helix: 1.66 (0.17), residues: 1015 sheet: -0.68 (0.22), residues: 596 loop : -0.22 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 488 HIS 0.005 0.001 HIS I 106 PHE 0.016 0.001 PHE J 26 TYR 0.020 0.001 TYR I 334 ARG 0.009 0.000 ARG I 96 Details of bonding type rmsd hydrogen bonds : bond 0.16857 ( 1052) hydrogen bonds : angle 6.76402 ( 3117) covalent geometry : bond 0.00269 (26562) covalent geometry : angle 0.57165 (36172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 793 time to evaluate : 2.931 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: A 1 MET cc_start: 0.3180 (mmm) cc_final: 0.2348 (tmm) REVERT: A 184 ASN cc_start: 0.5000 (m-40) cc_final: 0.2906 (m-40) REVERT: A 197 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6355 (mmm160) REVERT: B 61 ASN cc_start: 0.6906 (m-40) cc_final: 0.6614 (t0) REVERT: B 130 ASN cc_start: 0.8901 (m-40) cc_final: 0.8645 (m-40) REVERT: B 142 LEU cc_start: 0.7697 (mt) cc_final: 0.6685 (tt) REVERT: C 61 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.6610 (ttm170) REVERT: C 245 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7307 (p) REVERT: D 15 TYR cc_start: 0.6014 (m-80) cc_final: 0.5623 (m-10) REVERT: F 57 SER cc_start: 0.6764 (OUTLIER) cc_final: 0.6408 (t) REVERT: G 57 SER cc_start: 0.7268 (p) cc_final: 0.6711 (t) REVERT: G 161 SER cc_start: 0.4287 (OUTLIER) cc_final: 0.3835 (m) REVERT: G 215 ASN cc_start: 0.7514 (p0) cc_final: 0.7226 (p0) REVERT: G 254 LEU cc_start: 0.8216 (tp) cc_final: 0.7990 (tp) REVERT: H 32 ASP cc_start: 0.5641 (t0) cc_final: 0.5216 (t0) REVERT: H 146 VAL cc_start: 0.8450 (m) cc_final: 0.8177 (p) REVERT: H 171 HIS cc_start: 0.6545 (p-80) cc_final: 0.6306 (p90) REVERT: H 242 PHE cc_start: 0.6630 (m-80) cc_final: 0.6400 (m-10) REVERT: H 248 LYS cc_start: 0.7911 (mttp) cc_final: 0.7340 (mttp) REVERT: I 109 ILE cc_start: 0.6496 (mt) cc_final: 0.6134 (tp) REVERT: I 261 SER cc_start: 0.5542 (OUTLIER) cc_final: 0.5311 (p) REVERT: I 321 VAL cc_start: 0.7563 (t) cc_final: 0.6876 (t) REVERT: I 482 TRP cc_start: 0.7030 (p-90) cc_final: 0.6654 (p-90) REVERT: J 26 PHE cc_start: 0.7836 (m-80) cc_final: 0.7136 (m-80) REVERT: K 6 GLU cc_start: 0.8210 (tp30) cc_final: 0.7858 (tp30) outliers start: 75 outliers final: 12 residues processed: 837 average time/residue: 0.4585 time to fit residues: 580.8706 Evaluate side-chains 482 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 465 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 261 SER Chi-restraints excluded: chain J residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.0370 chunk 151 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 172 optimal weight: 0.0060 chunk 268 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN C 52 HIS C 171 HIS ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 30 ASN E 232 ASN F 30 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 233 HIS ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN I 104 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 GLN ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN J 81 HIS K 4 ASN ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN L 20 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.116267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.094843 restraints weight = 109283.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.097253 restraints weight = 66889.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.098619 restraints weight = 46363.169| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26562 Z= 0.159 Angle : 0.707 12.700 36172 Z= 0.368 Chirality : 0.044 0.231 3869 Planarity : 0.005 0.082 4399 Dihedral : 15.006 178.510 4287 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.13 % Favored : 94.53 % Rotamer: Outliers : 4.08 % Allowed : 23.33 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.07 (0.16), residues: 2943 helix: 1.05 (0.16), residues: 1027 sheet: -0.65 (0.22), residues: 577 loop : -0.30 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 363 HIS 0.015 0.001 HIS F 190 PHE 0.031 0.002 PHE L 61 TYR 0.022 0.002 TYR I 399 ARG 0.008 0.001 ARG L 71 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 1052) hydrogen bonds : angle 5.21560 ( 3117) covalent geometry : bond 0.00343 (26562) covalent geometry : angle 0.70658 (36172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 507 time to evaluate : 2.798 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: A 24 MET cc_start: 0.6405 (ttp) cc_final: 0.5899 (ttp) REVERT: A 39 MET cc_start: 0.8265 (tmm) cc_final: 0.7820 (ttt) REVERT: A 41 LEU cc_start: 0.7970 (mm) cc_final: 0.7490 (mm) REVERT: A 170 ARG cc_start: 0.7215 (ptt-90) cc_final: 0.6962 (ptt-90) REVERT: B 61 ASN cc_start: 0.6921 (m-40) cc_final: 0.6701 (t0) REVERT: B 142 LEU cc_start: 0.8476 (mt) cc_final: 0.7503 (tt) REVERT: B 183 GLU cc_start: 0.8076 (mp0) cc_final: 0.7578 (mp0) REVERT: C 46 TRP cc_start: 0.8276 (t-100) cc_final: 0.7082 (t-100) REVERT: C 61 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7719 (ttm170) REVERT: C 94 ASP cc_start: 0.8705 (t0) cc_final: 0.8352 (m-30) REVERT: C 137 MET cc_start: 0.8544 (tpp) cc_final: 0.8299 (tpp) REVERT: D 45 TYR cc_start: 0.8273 (m-80) cc_final: 0.7996 (m-10) REVERT: D 135 GLN cc_start: 0.6403 (mm110) cc_final: 0.6074 (mm-40) REVERT: D 137 MET cc_start: 0.7483 (tpp) cc_final: 0.7249 (tpp) REVERT: D 205 MET cc_start: 0.8177 (mmm) cc_final: 0.7824 (mmm) REVERT: D 206 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8339 (m-40) REVERT: E 33 ILE cc_start: 0.8440 (mm) cc_final: 0.7710 (tp) REVERT: E 54 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: E 64 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (tp) REVERT: E 77 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8098 (mtm110) REVERT: E 152 ASP cc_start: 0.8552 (p0) cc_final: 0.7913 (p0) REVERT: F 57 SER cc_start: 0.7835 (p) cc_final: 0.6322 (t) REVERT: G 35 ARG cc_start: 0.3002 (OUTLIER) cc_final: 0.2500 (mmm160) REVERT: G 218 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.7205 (m-40) REVERT: G 254 LEU cc_start: 0.8731 (tp) cc_final: 0.8280 (tp) REVERT: H 43 LYS cc_start: 0.8314 (pttp) cc_final: 0.7744 (mtmm) REVERT: H 55 VAL cc_start: 0.7724 (t) cc_final: 0.7381 (t) REVERT: H 234 PHE cc_start: 0.7959 (p90) cc_final: 0.7480 (p90) REVERT: H 248 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7940 (mptp) REVERT: H 249 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.6829 (p) REVERT: H 280 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9169 (ptpt) REVERT: H 283 GLN cc_start: 0.9243 (mt0) cc_final: 0.8928 (mm-40) REVERT: I 26 MET cc_start: 0.6986 (mtt) cc_final: 0.6734 (mtt) REVERT: I 204 PHE cc_start: 0.8123 (m-80) cc_final: 0.7819 (m-80) REVERT: I 231 VAL cc_start: 0.6378 (OUTLIER) cc_final: 0.5952 (t) REVERT: I 292 LYS cc_start: 0.8386 (mttt) cc_final: 0.8103 (pttt) REVERT: I 320 GLN cc_start: 0.8697 (tm130) cc_final: 0.8265 (tm-30) REVERT: I 321 VAL cc_start: 0.8189 (t) cc_final: 0.7907 (t) REVERT: I 363 TRP cc_start: 0.7531 (t-100) cc_final: 0.7228 (t-100) REVERT: I 451 GLU cc_start: 0.9006 (tt0) cc_final: 0.8558 (tm-30) REVERT: J 14 PHE cc_start: 0.8595 (t80) cc_final: 0.8238 (t80) REVERT: J 18 PHE cc_start: 0.9173 (t80) cc_final: 0.8839 (t80) REVERT: J 34 GLU cc_start: 0.4008 (pm20) cc_final: 0.3284 (mp0) REVERT: J 80 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: J 108 TYR cc_start: 0.5186 (OUTLIER) cc_final: 0.4056 (t80) REVERT: K 10 GLN cc_start: 0.8562 (mt0) cc_final: 0.7961 (mt0) REVERT: K 25 ASN cc_start: 0.6565 (OUTLIER) cc_final: 0.6348 (m-40) REVERT: L 15 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8086 (mm) REVERT: L 52 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8724 (mt) REVERT: L 88 LEU cc_start: 0.8990 (tp) cc_final: 0.8773 (tp) REVERT: L 96 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8922 (mp0) REVERT: L 100 TRP cc_start: 0.8253 (m-10) cc_final: 0.7898 (m-10) outliers start: 108 outliers final: 37 residues processed: 580 average time/residue: 0.4483 time to fit residues: 396.8471 Evaluate side-chains 472 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 420 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 148 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 90 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN E 229 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN F 256 GLN G 84 HIS G 181 GLN G 297 HIS I 88 HIS I 104 HIS I 210 HIS ** I 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 250 GLN I 313 ASN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN L 25 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.103500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.082365 restraints weight = 118451.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.084368 restraints weight = 73357.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.085728 restraints weight = 52055.402| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 26562 Z= 0.317 Angle : 0.850 13.671 36172 Z= 0.443 Chirality : 0.047 0.299 3869 Planarity : 0.006 0.080 4399 Dihedral : 15.110 179.303 4271 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 5.60 % Allowed : 22.16 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.15), residues: 2943 helix: 0.56 (0.15), residues: 1030 sheet: -0.77 (0.21), residues: 600 loop : -0.50 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP H 46 HIS 0.017 0.002 HIS C 190 PHE 0.058 0.003 PHE J 26 TYR 0.033 0.003 TYR K 54 ARG 0.019 0.001 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 1052) hydrogen bonds : angle 5.48614 ( 3117) covalent geometry : bond 0.00667 (26562) covalent geometry : angle 0.85004 (36172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 438 time to evaluate : 2.747 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: A 14 THR cc_start: 0.8924 (p) cc_final: 0.8688 (t) REVERT: A 24 MET cc_start: 0.7131 (ttp) cc_final: 0.6781 (ttp) REVERT: A 146 LYS cc_start: 0.6442 (tttt) cc_final: 0.6222 (tttp) REVERT: B 42 LEU cc_start: 0.7791 (tp) cc_final: 0.7582 (tp) REVERT: B 76 TYR cc_start: 0.8843 (t80) cc_final: 0.8544 (t80) REVERT: D 174 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7625 (tt0) REVERT: D 205 MET cc_start: 0.8717 (mmm) cc_final: 0.8507 (mmm) REVERT: E 38 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8082 (tttt) REVERT: E 65 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8041 (mtp85) REVERT: E 152 ASP cc_start: 0.8998 (p0) cc_final: 0.8715 (p0) REVERT: E 174 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8035 (mm-30) REVERT: F 30 ASN cc_start: 0.7500 (t0) cc_final: 0.7205 (t0) REVERT: F 57 SER cc_start: 0.7971 (p) cc_final: 0.6562 (m) REVERT: F 104 PHE cc_start: 0.7684 (m-10) cc_final: 0.7447 (m-80) REVERT: F 228 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: F 272 LEU cc_start: 0.8960 (tp) cc_final: 0.8247 (mm) REVERT: G 61 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7359 (mtp180) REVERT: G 135 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: G 266 GLN cc_start: 0.8160 (tp40) cc_final: 0.7926 (tp40) REVERT: H 43 LYS cc_start: 0.8241 (pttp) cc_final: 0.7894 (ptpp) REVERT: H 244 TYR cc_start: 0.6975 (t80) cc_final: 0.6609 (t80) REVERT: H 248 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8378 (mptp) REVERT: H 283 GLN cc_start: 0.9247 (mt0) cc_final: 0.8992 (mm-40) REVERT: I 31 MET cc_start: 0.6102 (ttm) cc_final: 0.5437 (ttt) REVERT: I 247 TRP cc_start: 0.8552 (m-10) cc_final: 0.8315 (m-10) REVERT: I 364 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: I 389 MET cc_start: 0.7882 (mmm) cc_final: 0.7566 (mmm) REVERT: I 410 MET cc_start: 0.7635 (ttp) cc_final: 0.7117 (ttp) REVERT: I 449 PHE cc_start: 0.8101 (t80) cc_final: 0.7852 (t80) REVERT: J 14 PHE cc_start: 0.8743 (t80) cc_final: 0.8518 (t80) REVERT: J 18 PHE cc_start: 0.9367 (t80) cc_final: 0.8991 (t80) REVERT: J 22 MET cc_start: 0.8770 (ppp) cc_final: 0.8286 (ppp) REVERT: J 46 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7716 (pp20) REVERT: J 80 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: J 100 TRP cc_start: 0.8810 (m-10) cc_final: 0.8385 (m-90) REVERT: J 108 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.4227 (t80) REVERT: K 10 GLN cc_start: 0.8485 (mt0) cc_final: 0.8268 (mt0) REVERT: K 23 LYS cc_start: 0.6424 (tppt) cc_final: 0.6186 (tppt) REVERT: L 61 PHE cc_start: 0.9162 (t80) cc_final: 0.8632 (t80) REVERT: L 71 ARG cc_start: 0.8415 (ttm170) cc_final: 0.7940 (ttm110) REVERT: L 88 LEU cc_start: 0.9070 (tp) cc_final: 0.8798 (tp) REVERT: L 90 LYS cc_start: 0.8432 (tptp) cc_final: 0.8086 (tptp) REVERT: L 95 GLN cc_start: 0.9229 (mm110) cc_final: 0.8931 (mm110) REVERT: L 96 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8995 (mp0) REVERT: L 100 TRP cc_start: 0.8375 (m-10) cc_final: 0.7952 (m-10) outliers start: 148 outliers final: 75 residues processed: 548 average time/residue: 0.4234 time to fit residues: 351.7062 Evaluate side-chains 473 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 389 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 LYS Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 196 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 277 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN I 104 HIS ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.104713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.083591 restraints weight = 116908.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.085646 restraints weight = 70821.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.086956 restraints weight = 49092.004| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26562 Z= 0.182 Angle : 0.702 14.535 36172 Z= 0.362 Chirality : 0.044 0.272 3869 Planarity : 0.005 0.085 4399 Dihedral : 15.065 179.262 4271 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.33 % Favored : 94.39 % Rotamer: Outliers : 4.35 % Allowed : 23.67 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.20 (0.16), residues: 2943 helix: 0.74 (0.16), residues: 1019 sheet: -0.63 (0.22), residues: 580 loop : -0.47 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 46 HIS 0.007 0.001 HIS I 104 PHE 0.028 0.002 PHE I 119 TYR 0.022 0.002 TYR B 29 ARG 0.010 0.001 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 1052) hydrogen bonds : angle 5.17565 ( 3117) covalent geometry : bond 0.00395 (26562) covalent geometry : angle 0.70152 (36172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 413 time to evaluate : 2.748 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: A 14 THR cc_start: 0.8890 (p) cc_final: 0.8558 (t) REVERT: A 20 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.7086 (t-90) REVERT: A 24 MET cc_start: 0.7417 (ttp) cc_final: 0.7106 (ttp) REVERT: A 39 MET cc_start: 0.8814 (tmm) cc_final: 0.8166 (tmm) REVERT: A 41 LEU cc_start: 0.8689 (tp) cc_final: 0.8432 (mm) REVERT: A 202 ASP cc_start: 0.8533 (m-30) cc_final: 0.7896 (t0) REVERT: B 42 LEU cc_start: 0.7755 (tp) cc_final: 0.7554 (tp) REVERT: B 76 TYR cc_start: 0.8698 (t80) cc_final: 0.8433 (t80) REVERT: B 131 PHE cc_start: 0.8534 (t80) cc_final: 0.8147 (m-80) REVERT: D 137 MET cc_start: 0.8041 (tpt) cc_final: 0.7721 (tpp) REVERT: D 174 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7501 (tt0) REVERT: D 204 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8415 (tt) REVERT: D 205 MET cc_start: 0.8565 (mmm) cc_final: 0.8312 (mmm) REVERT: D 207 LEU cc_start: 0.8974 (mt) cc_final: 0.8615 (mp) REVERT: E 38 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7953 (tttm) REVERT: E 65 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7953 (mtp85) REVERT: E 152 ASP cc_start: 0.8765 (p0) cc_final: 0.8441 (p0) REVERT: E 174 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: E 305 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7543 (ppp) REVERT: F 30 ASN cc_start: 0.7457 (t0) cc_final: 0.7078 (t0) REVERT: F 57 SER cc_start: 0.8139 (p) cc_final: 0.7724 (m) REVERT: F 104 PHE cc_start: 0.7478 (m-80) cc_final: 0.7267 (m-80) REVERT: F 228 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: F 272 LEU cc_start: 0.8947 (tp) cc_final: 0.8349 (mm) REVERT: G 266 GLN cc_start: 0.8093 (tp40) cc_final: 0.7844 (tp40) REVERT: H 144 MET cc_start: 0.7288 (mmp) cc_final: 0.6994 (mmp) REVERT: H 175 TYR cc_start: 0.8516 (p90) cc_final: 0.8240 (p90) REVERT: H 221 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: H 248 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8276 (mptp) REVERT: H 250 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6556 (ptpp) REVERT: H 280 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9079 (ptpt) REVERT: H 283 GLN cc_start: 0.9281 (mt0) cc_final: 0.9003 (mm-40) REVERT: I 247 TRP cc_start: 0.8710 (m-10) cc_final: 0.8058 (m-90) REVERT: I 449 PHE cc_start: 0.8183 (t80) cc_final: 0.7933 (t80) REVERT: I 465 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: J 18 PHE cc_start: 0.9382 (t80) cc_final: 0.9032 (t80) REVERT: J 22 MET cc_start: 0.8791 (ppp) cc_final: 0.8440 (ppp) REVERT: J 80 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: J 100 TRP cc_start: 0.8694 (m-10) cc_final: 0.8286 (m-90) REVERT: J 108 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.4721 (t80) REVERT: K 53 ASN cc_start: 0.8456 (p0) cc_final: 0.8225 (p0) REVERT: K 57 ASP cc_start: 0.7091 (t0) cc_final: 0.6859 (t0) REVERT: K 100 TRP cc_start: 0.9154 (m-10) cc_final: 0.8651 (m-10) REVERT: L 61 PHE cc_start: 0.9143 (t80) cc_final: 0.8373 (t80) REVERT: L 90 LYS cc_start: 0.8474 (tptp) cc_final: 0.7978 (tptt) REVERT: L 95 GLN cc_start: 0.9281 (mm110) cc_final: 0.9006 (mm110) REVERT: L 96 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8965 (mp0) outliers start: 115 outliers final: 62 residues processed: 497 average time/residue: 0.3918 time to fit residues: 300.0396 Evaluate side-chains 457 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 381 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 248 LYS Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 293 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 279 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 84 HIS G 233 HIS H 52 HIS I 104 HIS I 117 ASN ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 GLN ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN L 25 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.101629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.080700 restraints weight = 119845.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.082679 restraints weight = 73033.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.083925 restraints weight = 51342.268| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 26562 Z= 0.216 Angle : 0.731 14.765 36172 Z= 0.375 Chirality : 0.044 0.221 3869 Planarity : 0.005 0.103 4399 Dihedral : 15.147 179.224 4271 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.64 % Favored : 94.09 % Rotamer: Outliers : 5.03 % Allowed : 23.06 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.16), residues: 2943 helix: 0.60 (0.16), residues: 1023 sheet: -0.69 (0.22), residues: 599 loop : -0.59 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP H 46 HIS 0.008 0.001 HIS I 104 PHE 0.023 0.002 PHE J 14 TYR 0.029 0.002 TYR B 29 ARG 0.010 0.001 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1052) hydrogen bonds : angle 5.22397 ( 3117) covalent geometry : bond 0.00471 (26562) covalent geometry : angle 0.73115 (36172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 398 time to evaluate : 4.496 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 14 THR cc_start: 0.8992 (p) cc_final: 0.8713 (t) REVERT: A 20 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7111 (t-90) REVERT: A 39 MET cc_start: 0.8804 (tmm) cc_final: 0.8261 (tmm) REVERT: A 202 ASP cc_start: 0.8665 (m-30) cc_final: 0.8031 (t0) REVERT: B 63 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5077 (mt) REVERT: B 76 TYR cc_start: 0.8779 (t80) cc_final: 0.8550 (t80) REVERT: B 131 PHE cc_start: 0.8641 (t80) cc_final: 0.8248 (m-80) REVERT: B 142 LEU cc_start: 0.7762 (mp) cc_final: 0.6708 (tp) REVERT: C 54 PHE cc_start: 0.7970 (m-80) cc_final: 0.7694 (m-80) REVERT: C 55 VAL cc_start: 0.9071 (t) cc_final: 0.8806 (t) REVERT: C 234 PHE cc_start: 0.7903 (m-10) cc_final: 0.7535 (m-10) REVERT: D 137 MET cc_start: 0.8233 (tpt) cc_final: 0.7951 (tpp) REVERT: E 65 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7819 (mtp85) REVERT: E 137 MET cc_start: 0.7688 (tmm) cc_final: 0.7422 (tmm) REVERT: E 144 MET cc_start: 0.8784 (mmm) cc_final: 0.8094 (mmm) REVERT: E 152 ASP cc_start: 0.8839 (p0) cc_final: 0.8291 (p0) REVERT: E 305 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7498 (ppp) REVERT: F 30 ASN cc_start: 0.7625 (t0) cc_final: 0.7251 (t0) REVERT: F 57 SER cc_start: 0.8332 (p) cc_final: 0.8069 (m) REVERT: F 228 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: F 272 LEU cc_start: 0.9042 (tp) cc_final: 0.8445 (mm) REVERT: G 266 GLN cc_start: 0.8180 (tp40) cc_final: 0.7926 (tp40) REVERT: H 88 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7916 (tp) REVERT: H 175 TYR cc_start: 0.8496 (p90) cc_final: 0.8192 (p90) REVERT: H 221 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: H 250 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.6165 (ptpp) REVERT: I 188 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7658 (p0) REVERT: I 244 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7707 (pt0) REVERT: I 247 TRP cc_start: 0.8765 (m-10) cc_final: 0.8458 (m-90) REVERT: I 449 PHE cc_start: 0.8367 (t80) cc_final: 0.7905 (t80) REVERT: I 465 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: I 482 TRP cc_start: 0.7522 (p-90) cc_final: 0.7280 (p-90) REVERT: J 18 PHE cc_start: 0.9398 (t80) cc_final: 0.9014 (t80) REVERT: J 22 MET cc_start: 0.8842 (ppp) cc_final: 0.8482 (ppp) REVERT: J 46 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7902 (pp20) REVERT: J 80 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: J 81 HIS cc_start: 0.8741 (m-70) cc_final: 0.8517 (m90) REVERT: J 100 TRP cc_start: 0.8661 (m-10) cc_final: 0.8233 (m-90) REVERT: J 108 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.4677 (t80) REVERT: K 53 ASN cc_start: 0.8597 (p0) cc_final: 0.8391 (p0) REVERT: K 91 LYS cc_start: 0.9049 (mtmm) cc_final: 0.8795 (mtmm) REVERT: K 100 TRP cc_start: 0.9178 (m-10) cc_final: 0.8552 (m-10) REVERT: L 53 ASN cc_start: 0.8857 (p0) cc_final: 0.8649 (p0) REVERT: L 61 PHE cc_start: 0.9035 (t80) cc_final: 0.8404 (t80) REVERT: L 66 SER cc_start: 0.9770 (m) cc_final: 0.9470 (t) REVERT: L 71 ARG cc_start: 0.8279 (ttm170) cc_final: 0.8017 (mtp-110) REVERT: L 75 ASN cc_start: 0.8858 (t0) cc_final: 0.8309 (t0) REVERT: L 90 LYS cc_start: 0.8511 (tptp) cc_final: 0.7983 (tptt) REVERT: L 95 GLN cc_start: 0.9293 (mm110) cc_final: 0.9004 (mm110) REVERT: L 96 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8945 (mp0) REVERT: L 100 TRP cc_start: 0.8104 (m-10) cc_final: 0.7847 (m-10) outliers start: 133 outliers final: 84 residues processed: 494 average time/residue: 0.5046 time to fit residues: 394.6639 Evaluate side-chains 467 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 371 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 GLN Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 54 optimal weight: 10.0000 chunk 116 optimal weight: 0.0970 chunk 51 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 223 optimal weight: 6.9990 chunk 210 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 136 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN I 104 HIS I 149 HIS ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.104389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.083451 restraints weight = 116011.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.085498 restraints weight = 71117.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.086672 restraints weight = 49198.686| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26562 Z= 0.133 Angle : 0.688 16.399 36172 Z= 0.345 Chirality : 0.043 0.198 3869 Planarity : 0.005 0.083 4399 Dihedral : 15.043 177.852 4271 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.03 % Favored : 94.73 % Rotamer: Outliers : 3.89 % Allowed : 24.31 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.23 (0.16), residues: 2943 helix: 0.68 (0.16), residues: 1024 sheet: -0.51 (0.22), residues: 572 loop : -0.54 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP H 46 HIS 0.007 0.001 HIS K 81 PHE 0.048 0.002 PHE J 26 TYR 0.033 0.002 TYR B 29 ARG 0.013 0.001 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1052) hydrogen bonds : angle 5.01774 ( 3117) covalent geometry : bond 0.00295 (26562) covalent geometry : angle 0.68807 (36172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 412 time to evaluate : 3.192 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: A 14 THR cc_start: 0.8955 (p) cc_final: 0.8750 (t) REVERT: A 20 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6809 (t-90) REVERT: A 202 ASP cc_start: 0.8585 (m-30) cc_final: 0.7947 (t0) REVERT: B 63 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5151 (mt) REVERT: C 54 PHE cc_start: 0.7891 (m-80) cc_final: 0.7468 (m-80) REVERT: C 234 PHE cc_start: 0.7877 (m-10) cc_final: 0.7653 (m-10) REVERT: D 137 MET cc_start: 0.8212 (tpt) cc_final: 0.7965 (tpp) REVERT: D 152 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8516 (p0) REVERT: E 38 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7963 (tttt) REVERT: E 137 MET cc_start: 0.7723 (tmm) cc_final: 0.7480 (tmm) REVERT: E 152 ASP cc_start: 0.8634 (p0) cc_final: 0.8168 (p0) REVERT: E 250 LYS cc_start: 0.8879 (ptpt) cc_final: 0.7764 (ptpt) REVERT: E 305 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7559 (ppp) REVERT: F 30 ASN cc_start: 0.7375 (t0) cc_final: 0.7102 (t0) REVERT: F 57 SER cc_start: 0.8382 (p) cc_final: 0.8149 (m) REVERT: F 175 TYR cc_start: 0.7923 (p90) cc_final: 0.7079 (p90) REVERT: F 228 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: F 272 LEU cc_start: 0.8983 (tp) cc_final: 0.8479 (mm) REVERT: G 144 MET cc_start: 0.7295 (mtp) cc_final: 0.7089 (ttt) REVERT: G 266 GLN cc_start: 0.8057 (tp40) cc_final: 0.7705 (tp40) REVERT: H 144 MET cc_start: 0.7391 (mmp) cc_final: 0.6973 (mmp) REVERT: H 200 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8338 (ttp) REVERT: H 221 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: H 237 TYR cc_start: 0.4059 (OUTLIER) cc_final: 0.3790 (m-80) REVERT: H 250 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5758 (ptpp) REVERT: I 31 MET cc_start: 0.6001 (ttm) cc_final: 0.5792 (mmm) REVERT: I 244 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7715 (pt0) REVERT: I 247 TRP cc_start: 0.8746 (m-10) cc_final: 0.8526 (m-90) REVERT: I 410 MET cc_start: 0.7005 (ttt) cc_final: 0.6690 (ptm) REVERT: I 440 LEU cc_start: 0.9293 (mt) cc_final: 0.9035 (mm) REVERT: I 449 PHE cc_start: 0.8265 (t80) cc_final: 0.8012 (t80) REVERT: I 482 TRP cc_start: 0.7349 (p-90) cc_final: 0.7127 (p-90) REVERT: J 14 PHE cc_start: 0.8638 (t80) cc_final: 0.8349 (t80) REVERT: J 18 PHE cc_start: 0.9403 (t80) cc_final: 0.9068 (t80) REVERT: J 22 MET cc_start: 0.8882 (ppp) cc_final: 0.8518 (ppp) REVERT: J 80 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: J 81 HIS cc_start: 0.8547 (m-70) cc_final: 0.8135 (m-70) REVERT: J 100 TRP cc_start: 0.8616 (m-10) cc_final: 0.8189 (m-90) REVERT: J 108 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.4729 (t80) REVERT: K 6 GLU cc_start: 0.8440 (pm20) cc_final: 0.7789 (tp30) REVERT: K 100 TRP cc_start: 0.9080 (m-10) cc_final: 0.8357 (m-10) REVERT: L 22 MET cc_start: 0.7246 (mtp) cc_final: 0.6941 (mtt) REVERT: L 53 ASN cc_start: 0.8883 (p0) cc_final: 0.8499 (p0) REVERT: L 61 PHE cc_start: 0.9019 (t80) cc_final: 0.8450 (t80) REVERT: L 66 SER cc_start: 0.9743 (m) cc_final: 0.9395 (t) REVERT: L 75 ASN cc_start: 0.8875 (t0) cc_final: 0.8328 (t0) REVERT: L 90 LYS cc_start: 0.8339 (tptp) cc_final: 0.7622 (tptt) REVERT: L 95 GLN cc_start: 0.9284 (mm110) cc_final: 0.8983 (mm110) REVERT: L 96 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8876 (mp0) outliers start: 103 outliers final: 60 residues processed: 483 average time/residue: 0.4987 time to fit residues: 381.2714 Evaluate side-chains 455 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 383 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 GLN Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 230 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN B 43 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** 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 = 0.4201 r_free = 0.4201 target = 0.099037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.078266 restraints weight = 121801.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.080231 restraints weight = 75040.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.081439 restraints weight = 52503.644| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.7246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26562 Z= 0.263 Angle : 0.791 16.833 36172 Z= 0.404 Chirality : 0.045 0.228 3869 Planarity : 0.006 0.120 4399 Dihedral : 15.284 179.823 4271 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.35 % Favored : 93.37 % Rotamer: Outliers : 4.69 % Allowed : 24.65 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.59 (0.16), residues: 2943 helix: 0.37 (0.16), residues: 1018 sheet: -0.77 (0.22), residues: 591 loop : -0.69 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP H 46 HIS 0.008 0.002 HIS F 190 PHE 0.031 0.002 PHE D 221 TYR 0.028 0.002 TYR I 442 ARG 0.015 0.001 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1052) hydrogen bonds : angle 5.38759 ( 3117) covalent geometry : bond 0.00565 (26562) covalent geometry : angle 0.79051 (36172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 370 time to evaluate : 4.254 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: A 20 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.7099 (t-90) REVERT: A 24 MET cc_start: 0.7906 (ttp) cc_final: 0.7481 (ttp) REVERT: A 48 ASN cc_start: 0.8233 (m-40) cc_final: 0.7767 (t0) REVERT: A 195 MET cc_start: 0.7546 (pmm) cc_final: 0.7326 (pmm) REVERT: A 202 ASP cc_start: 0.8744 (m-30) cc_final: 0.8156 (t0) REVERT: B 63 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5382 (mt) REVERT: C 54 PHE cc_start: 0.7925 (m-80) cc_final: 0.7497 (m-80) REVERT: C 144 MET cc_start: 0.8688 (tpp) cc_final: 0.8285 (tpp) REVERT: D 137 MET cc_start: 0.8368 (tpt) cc_final: 0.7973 (tpp) REVERT: E 38 LYS cc_start: 0.8364 (tttm) cc_final: 0.8127 (tttm) REVERT: E 137 MET cc_start: 0.7516 (tmm) cc_final: 0.7230 (tmm) REVERT: E 152 ASP cc_start: 0.8967 (p0) cc_final: 0.8541 (p0) REVERT: E 207 LEU cc_start: 0.9207 (tp) cc_final: 0.8932 (tp) REVERT: H 43 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7896 (mttp) REVERT: H 88 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7972 (tp) REVERT: H 221 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: H 250 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.5998 (ptpp) REVERT: I 31 MET cc_start: 0.6525 (ttm) cc_final: 0.4761 (ttm) REVERT: I 35 ARG cc_start: 0.8131 (mmt180) cc_final: 0.7674 (mmm-85) REVERT: I 449 PHE cc_start: 0.8380 (t80) cc_final: 0.7884 (t80) REVERT: I 451 GLU cc_start: 0.9105 (tt0) cc_final: 0.8638 (tm-30) REVERT: I 465 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: I 482 TRP cc_start: 0.7537 (p-90) cc_final: 0.7077 (p-90) REVERT: J 14 PHE cc_start: 0.8901 (t80) cc_final: 0.8621 (t80) REVERT: J 18 PHE cc_start: 0.9410 (t80) cc_final: 0.9121 (t80) REVERT: J 22 MET cc_start: 0.8843 (ppp) cc_final: 0.8338 (ppp) REVERT: J 46 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8107 (pp20) REVERT: J 80 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: J 81 HIS cc_start: 0.8816 (m-70) cc_final: 0.8493 (m90) REVERT: J 100 TRP cc_start: 0.8614 (m-10) cc_final: 0.8125 (m-90) REVERT: J 108 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.4983 (t80) REVERT: K 22 MET cc_start: 0.6654 (ptm) cc_final: 0.6219 (ppp) REVERT: K 62 LYS cc_start: 0.9437 (mttm) cc_final: 0.9177 (mtmm) REVERT: L 53 ASN cc_start: 0.8890 (p0) cc_final: 0.8577 (p0) REVERT: L 66 SER cc_start: 0.9780 (m) cc_final: 0.9466 (t) REVERT: L 75 ASN cc_start: 0.8967 (t0) cc_final: 0.8420 (t0) outliers start: 124 outliers final: 85 residues processed: 457 average time/residue: 0.4153 time to fit residues: 300.0449 Evaluate side-chains 437 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 343 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 GLN Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 81 HIS Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 33 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.102677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.081898 restraints weight = 117153.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.083880 restraints weight = 71136.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.085173 restraints weight = 49082.607| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26562 Z= 0.144 Angle : 0.741 17.433 36172 Z= 0.371 Chirality : 0.044 0.250 3869 Planarity : 0.005 0.088 4399 Dihedral : 15.137 179.172 4270 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 3.71 % Allowed : 25.82 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.51 (0.16), residues: 2943 helix: 0.39 (0.16), residues: 1024 sheet: -0.70 (0.22), residues: 567 loop : -0.62 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP H 46 HIS 0.005 0.001 HIS I 104 PHE 0.040 0.002 PHE I 338 TYR 0.032 0.002 TYR E 182 ARG 0.012 0.001 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1052) hydrogen bonds : angle 5.17184 ( 3117) covalent geometry : bond 0.00320 (26562) covalent geometry : angle 0.74055 (36172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 386 time to evaluate : 2.957 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 20 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.6920 (t-90) REVERT: A 41 LEU cc_start: 0.8799 (pp) cc_final: 0.8168 (tp) REVERT: A 48 ASN cc_start: 0.8270 (m-40) cc_final: 0.7620 (t0) REVERT: A 78 LYS cc_start: 0.7179 (mtpt) cc_final: 0.6931 (mtmt) REVERT: A 195 MET cc_start: 0.7590 (pmm) cc_final: 0.7092 (pmm) REVERT: A 202 ASP cc_start: 0.8633 (m-30) cc_final: 0.7994 (t0) REVERT: B 46 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7336 (tptt) REVERT: B 63 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5889 (mt) REVERT: B 203 MET cc_start: 0.7946 (ptp) cc_final: 0.7590 (ptp) REVERT: B 204 MET cc_start: 0.8815 (ptp) cc_final: 0.7992 (pmm) REVERT: C 54 PHE cc_start: 0.7881 (m-80) cc_final: 0.7504 (m-80) REVERT: D 137 MET cc_start: 0.8283 (tpt) cc_final: 0.7911 (tpp) REVERT: D 140 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 157 LEU cc_start: 0.8871 (mm) cc_final: 0.8413 (mt) REVERT: E 38 LYS cc_start: 0.8194 (tttm) cc_final: 0.7935 (tttm) REVERT: E 137 MET cc_start: 0.7539 (tmm) cc_final: 0.7312 (tmm) REVERT: E 152 ASP cc_start: 0.8687 (p0) cc_final: 0.8130 (p0) REVERT: F 30 ASN cc_start: 0.7553 (t0) cc_final: 0.7146 (t0) REVERT: F 175 TYR cc_start: 0.7809 (p90) cc_final: 0.7086 (p90) REVERT: F 303 ASN cc_start: 0.9226 (m-40) cc_final: 0.8988 (p0) REVERT: H 43 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7762 (mttp) REVERT: H 60 ILE cc_start: 0.9373 (pt) cc_final: 0.9164 (pt) REVERT: H 137 MET cc_start: 0.7842 (tpp) cc_final: 0.7311 (tpp) REVERT: H 142 MET cc_start: 0.7151 (ptp) cc_final: 0.6607 (pmm) REVERT: H 144 MET cc_start: 0.6894 (mmp) cc_final: 0.6558 (mmp) REVERT: H 221 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: H 234 PHE cc_start: 0.7825 (p90) cc_final: 0.7139 (p90) REVERT: H 237 TYR cc_start: 0.4065 (OUTLIER) cc_final: 0.3456 (m-80) REVERT: H 240 TYR cc_start: 0.6047 (m-80) cc_final: 0.5728 (m-10) REVERT: H 250 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5765 (ptpp) REVERT: I 35 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7875 (mmm160) REVERT: I 247 TRP cc_start: 0.8914 (m-10) cc_final: 0.8661 (m-90) REVERT: I 410 MET cc_start: 0.7062 (ttt) cc_final: 0.6653 (ptm) REVERT: I 440 LEU cc_start: 0.9311 (mt) cc_final: 0.9035 (mm) REVERT: I 449 PHE cc_start: 0.8229 (t80) cc_final: 0.7764 (t80) REVERT: I 451 GLU cc_start: 0.9087 (tt0) cc_final: 0.8601 (tm-30) REVERT: I 482 TRP cc_start: 0.7388 (p-90) cc_final: 0.6921 (p-90) REVERT: J 14 PHE cc_start: 0.8777 (t80) cc_final: 0.8497 (t80) REVERT: J 18 PHE cc_start: 0.9452 (t80) cc_final: 0.9211 (t80) REVERT: J 22 MET cc_start: 0.8897 (ppp) cc_final: 0.8452 (ppp) REVERT: J 46 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7692 (pt0) REVERT: J 62 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8367 (mtmm) REVERT: J 80 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: J 100 TRP cc_start: 0.8640 (m-10) cc_final: 0.8149 (m-90) REVERT: J 108 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.4908 (t80) REVERT: K 22 MET cc_start: 0.6423 (ptm) cc_final: 0.6055 (ppp) REVERT: K 62 LYS cc_start: 0.9417 (mttm) cc_final: 0.9190 (mttp) REVERT: L 22 MET cc_start: 0.7270 (mtp) cc_final: 0.6942 (mtt) REVERT: L 53 ASN cc_start: 0.8854 (p0) cc_final: 0.8507 (p0) REVERT: L 66 SER cc_start: 0.9663 (m) cc_final: 0.9326 (t) REVERT: L 75 ASN cc_start: 0.8995 (t0) cc_final: 0.8462 (t0) REVERT: L 95 GLN cc_start: 0.9263 (mm110) cc_final: 0.8980 (mm110) outliers start: 98 outliers final: 66 residues processed: 456 average time/residue: 0.4045 time to fit residues: 287.7211 Evaluate side-chains 437 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 361 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 320 GLN Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 81 HIS Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 55 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.096889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.076490 restraints weight = 124031.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.078305 restraints weight = 76383.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.079499 restraints weight = 52902.773| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.8097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26562 Z= 0.290 Angle : 0.855 17.864 36172 Z= 0.438 Chirality : 0.048 0.329 3869 Planarity : 0.006 0.127 4399 Dihedral : 15.414 179.542 4265 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.80 % Favored : 92.97 % Rotamer: Outliers : 4.39 % Allowed : 25.78 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.94 (0.15), residues: 2943 helix: -0.00 (0.16), residues: 1018 sheet: -0.83 (0.22), residues: 570 loop : -0.90 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP H 46 HIS 0.008 0.002 HIS F 84 PHE 0.033 0.003 PHE D 221 TYR 0.061 0.003 TYR H 244 ARG 0.008 0.001 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 1052) hydrogen bonds : angle 5.63268 ( 3117) covalent geometry : bond 0.00623 (26562) covalent geometry : angle 0.85476 (36172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 357 time to evaluate : 3.059 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: A 20 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7187 (t-90) REVERT: A 41 LEU cc_start: 0.8958 (pp) cc_final: 0.8348 (tp) REVERT: A 48 ASN cc_start: 0.8338 (m-40) cc_final: 0.7588 (t0) REVERT: A 69 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7610 (ttp80) REVERT: A 135 CYS cc_start: 0.6131 (t) cc_final: 0.5597 (m) REVERT: A 202 ASP cc_start: 0.8971 (m-30) cc_final: 0.8281 (t0) REVERT: B 63 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6267 (mt) REVERT: B 86 TYR cc_start: 0.8594 (m-80) cc_final: 0.8067 (m-80) REVERT: B 203 MET cc_start: 0.8207 (ptp) cc_final: 0.7919 (ptp) REVERT: D 38 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8269 (tptp) REVERT: D 137 MET cc_start: 0.8286 (tpt) cc_final: 0.7969 (tpp) REVERT: D 238 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9051 (tp) REVERT: E 38 LYS cc_start: 0.8169 (tttm) cc_final: 0.7810 (tttt) REVERT: E 152 ASP cc_start: 0.8948 (p0) cc_final: 0.8498 (p0) REVERT: E 207 LEU cc_start: 0.9174 (tp) cc_final: 0.8917 (tp) REVERT: F 175 TYR cc_start: 0.8117 (p90) cc_final: 0.7293 (p90) REVERT: F 248 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7856 (mttt) REVERT: F 272 LEU cc_start: 0.9073 (tp) cc_final: 0.8362 (mt) REVERT: H 43 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8273 (mttp) REVERT: H 142 MET cc_start: 0.7562 (ptp) cc_final: 0.6664 (pmm) REVERT: H 221 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: H 234 PHE cc_start: 0.7829 (p90) cc_final: 0.7228 (p90) REVERT: H 237 TYR cc_start: 0.4591 (OUTLIER) cc_final: 0.3777 (m-80) REVERT: H 250 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6056 (ptpp) REVERT: I 31 MET cc_start: 0.7098 (ttm) cc_final: 0.5290 (ttt) REVERT: I 35 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7661 (mmm-85) REVERT: I 188 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7810 (p0) REVERT: I 449 PHE cc_start: 0.8435 (t80) cc_final: 0.8174 (t80) REVERT: I 465 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6718 (m-80) REVERT: I 482 TRP cc_start: 0.7679 (p-90) cc_final: 0.7293 (p-90) REVERT: J 14 PHE cc_start: 0.9023 (t80) cc_final: 0.8733 (t80) REVERT: J 18 PHE cc_start: 0.9417 (t80) cc_final: 0.9112 (t80) REVERT: J 22 MET cc_start: 0.8867 (ppp) cc_final: 0.8424 (ppp) REVERT: J 46 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8086 (pt0) REVERT: J 80 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8817 (mt-10) REVERT: J 82 GLN cc_start: 0.8775 (mm110) cc_final: 0.8404 (mm110) REVERT: J 100 TRP cc_start: 0.8584 (m-10) cc_final: 0.8026 (m-90) REVERT: J 108 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.5029 (t80) REVERT: K 49 ARG cc_start: 0.9039 (tmm160) cc_final: 0.8779 (tmm-80) REVERT: K 52 LEU cc_start: 0.9202 (mt) cc_final: 0.8975 (mt) REVERT: K 79 ASN cc_start: 0.9159 (m-40) cc_final: 0.8872 (m-40) REVERT: L 22 MET cc_start: 0.7221 (mtp) cc_final: 0.6883 (mtt) REVERT: L 53 ASN cc_start: 0.8810 (p0) cc_final: 0.8509 (p0) REVERT: L 66 SER cc_start: 0.9757 (m) cc_final: 0.9397 (t) REVERT: L 75 ASN cc_start: 0.9006 (t0) cc_final: 0.8550 (t0) outliers start: 116 outliers final: 79 residues processed: 443 average time/residue: 0.3912 time to fit residues: 270.9514 Evaluate side-chains 432 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 340 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 320 GLN Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 81 HIS Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 284 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.097186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.076860 restraints weight = 122898.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.078742 restraints weight = 75177.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.079950 restraints weight = 52867.525| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.8145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.324 26562 Z= 0.339 Angle : 0.965 65.880 36172 Z= 0.506 Chirality : 0.048 0.358 3869 Planarity : 0.007 0.195 4399 Dihedral : 15.415 179.481 4265 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 33.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.90 % Favored : 92.86 % Rotamer: Outliers : 3.93 % Allowed : 26.65 % Favored : 69.41 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.91 % 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: -0.99 (0.15), residues: 2943 helix: -0.03 (0.16), residues: 1018 sheet: -0.88 (0.22), residues: 572 loop : -0.92 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP H 46 HIS 0.024 0.002 HIS J 81 PHE 0.033 0.003 PHE K 26 TYR 0.050 0.003 TYR H 244 ARG 0.024 0.001 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 1052) hydrogen bonds : angle 5.63272 ( 3117) covalent geometry : bond 0.00781 (26562) covalent geometry : angle 0.96488 (36172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 339 time to evaluate : 2.733 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: A 20 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.7179 (t-90) REVERT: A 41 LEU cc_start: 0.8944 (pp) cc_final: 0.8248 (mt) REVERT: A 48 ASN cc_start: 0.8312 (m-40) cc_final: 0.7641 (t0) REVERT: A 69 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7605 (ttp80) REVERT: A 135 CYS cc_start: 0.6140 (t) cc_final: 0.5599 (m) REVERT: A 202 ASP cc_start: 0.8978 (m-30) cc_final: 0.8284 (t0) REVERT: B 63 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6261 (mt) REVERT: B 86 TYR cc_start: 0.8669 (m-80) cc_final: 0.8069 (m-80) REVERT: B 203 MET cc_start: 0.8183 (ptp) cc_final: 0.7906 (ptp) REVERT: C 144 MET cc_start: 0.8412 (tpp) cc_final: 0.8069 (tpp) REVERT: D 38 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8300 (tptp) REVERT: D 137 MET cc_start: 0.8187 (tpt) cc_final: 0.7956 (tpp) REVERT: D 238 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9051 (tp) REVERT: E 38 LYS cc_start: 0.8177 (tttm) cc_final: 0.7810 (tttt) REVERT: E 152 ASP cc_start: 0.8993 (p0) cc_final: 0.8515 (p0) REVERT: E 207 LEU cc_start: 0.9186 (tp) cc_final: 0.8913 (tp) REVERT: F 175 TYR cc_start: 0.8124 (p90) cc_final: 0.7296 (p90) REVERT: F 248 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7839 (mttt) REVERT: F 272 LEU cc_start: 0.9071 (tp) cc_final: 0.8356 (mt) REVERT: H 43 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8263 (mttp) REVERT: H 142 MET cc_start: 0.7564 (ptp) cc_final: 0.6677 (pmm) REVERT: H 221 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: H 234 PHE cc_start: 0.7859 (p90) cc_final: 0.7227 (p90) REVERT: H 237 TYR cc_start: 0.4604 (OUTLIER) cc_final: 0.3800 (m-80) REVERT: H 250 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6052 (ptpp) REVERT: I 31 MET cc_start: 0.7095 (ttm) cc_final: 0.5289 (ttt) REVERT: I 35 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7687 (mmm-85) REVERT: I 188 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7808 (p0) REVERT: I 295 LYS cc_start: 0.4969 (OUTLIER) cc_final: 0.4751 (pttm) REVERT: I 449 PHE cc_start: 0.8412 (t80) cc_final: 0.8145 (t80) REVERT: I 465 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: I 482 TRP cc_start: 0.7677 (p-90) cc_final: 0.7306 (p-90) REVERT: J 14 PHE cc_start: 0.9018 (t80) cc_final: 0.8724 (t80) REVERT: J 18 PHE cc_start: 0.9403 (t80) cc_final: 0.9093 (t80) REVERT: J 22 MET cc_start: 0.8848 (ppp) cc_final: 0.8417 (ppp) REVERT: J 46 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8088 (pt0) REVERT: J 80 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8819 (mt-10) REVERT: J 82 GLN cc_start: 0.8748 (mm110) cc_final: 0.8376 (mm110) REVERT: J 100 TRP cc_start: 0.8556 (m-10) cc_final: 0.8032 (m-90) REVERT: J 108 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.5069 (t80) REVERT: K 49 ARG cc_start: 0.9019 (tmm160) cc_final: 0.8738 (tmm-80) REVERT: K 79 ASN cc_start: 0.9169 (m-40) cc_final: 0.8817 (m-40) REVERT: L 22 MET cc_start: 0.7215 (mtp) cc_final: 0.6884 (mtt) REVERT: L 53 ASN cc_start: 0.8797 (p0) cc_final: 0.8499 (p0) REVERT: L 66 SER cc_start: 0.9729 (m) cc_final: 0.9360 (t) REVERT: L 75 ASN cc_start: 0.8996 (t0) cc_final: 0.8544 (t0) outliers start: 104 outliers final: 84 residues processed: 416 average time/residue: 0.3666 time to fit residues: 240.6578 Evaluate side-chains 436 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 338 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 264 CYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 274 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 320 GLN Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 81 HIS Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 193 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 250 optimal weight: 0.0370 chunk 97 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.101722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.081155 restraints weight = 118018.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.083162 restraints weight = 71393.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.084341 restraints weight = 49641.357| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.8039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26562 Z= 0.149 Angle : 0.785 17.560 36172 Z= 0.395 Chirality : 0.046 0.299 3869 Planarity : 0.005 0.093 4399 Dihedral : 15.245 177.285 4265 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.20 % Favored : 94.60 % Rotamer: Outliers : 3.14 % Allowed : 27.45 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.74 (0.16), residues: 2943 helix: 0.14 (0.16), residues: 1017 sheet: -0.78 (0.23), residues: 542 loop : -0.73 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP H 46 HIS 0.011 0.001 HIS J 81 PHE 0.031 0.002 PHE L 61 TYR 0.041 0.002 TYR E 182 ARG 0.014 0.001 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 1052) hydrogen bonds : angle 5.30361 ( 3117) covalent geometry : bond 0.00330 (26562) covalent geometry : angle 0.78491 (36172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10206.15 seconds wall clock time: 181 minutes 43.14 seconds (10903.14 seconds total)