Starting phenix.real_space_refine on Mon Jun 23 13:49:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gan_29901/06_2025/8gan_29901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gan_29901/06_2025/8gan_29901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gan_29901/06_2025/8gan_29901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gan_29901/06_2025/8gan_29901.map" model { file = "/net/cci-nas-00/data/ceres_data/8gan_29901/06_2025/8gan_29901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gan_29901/06_2025/8gan_29901.cif" } resolution = 3.26 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 112 5.16 5 C 16933 2.51 5 N 4952 2.21 5 O 5536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27669 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "C" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "D" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "F" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2173 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "H" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4555 Classifications: {'peptide': 582} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 558} Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 916 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 17, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 25, 'rna3p': 17} Chain: "L" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1093 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "O" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "Q" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 429 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Time building chain proxies: 16.98, per 1000 atoms: 0.61 Number of scatterers: 27669 At special positions: 0 Unit cell: (108.239, 109.645, 215.072, 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 112 16.00 P 136 15.00 O 5536 8.00 N 4952 7.00 C 16933 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: 7.19 Conformation dependent library (CDL) restraints added in 3.2 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5746 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 34 sheets defined 37.3% alpha, 11.0% beta 30 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 12.69 Creating SS restraints... Processing helix chain 'A' and resid 42 through 57 removed outlier: 4.171A pdb=" N LEU A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.731A pdb=" N GLU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.637A pdb=" N LEU A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'B' and resid 24 through 27 removed outlier: 3.520A pdb=" N GLY B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 27' Processing helix chain 'B' and resid 42 through 57 removed outlier: 4.170A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 91 through 106 removed outlier: 3.732A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 195 through 208 Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.638A pdb=" N LEU B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'C' and resid 24 through 27 removed outlier: 3.924A pdb=" N GLY C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 27' Processing helix chain 'C' and resid 42 through 57 removed outlier: 4.170A pdb=" N LEU C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 91 through 106 removed outlier: 3.731A pdb=" N GLU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 239 through 246 removed outlier: 3.637A pdb=" N LEU C 243 " --> pdb=" O PRO C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'D' and resid 24 through 27 removed outlier: 3.828A pdb=" N GLY D 27 " --> pdb=" O PRO D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 42 through 57 removed outlier: 4.171A pdb=" N LEU D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 82 Processing helix chain 'D' and resid 91 through 106 removed outlier: 3.730A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 186 through 193 Processing helix chain 'D' and resid 195 through 208 Processing helix chain 'D' and resid 239 through 246 removed outlier: 3.638A pdb=" N LEU D 243 " --> pdb=" O PRO D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.712A pdb=" N GLY E 27 " --> pdb=" O PRO E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 57 removed outlier: 4.170A pdb=" N LEU E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 91 through 106 removed outlier: 3.731A pdb=" N GLU E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 186 through 193 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 239 through 246 removed outlier: 3.637A pdb=" N LEU E 243 " --> pdb=" O PRO E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'F' and resid 42 through 57 removed outlier: 4.171A pdb=" N LEU F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 91 through 106 removed outlier: 3.731A pdb=" N GLU F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 186 through 193 Processing helix chain 'F' and resid 195 through 208 Processing helix chain 'F' and resid 239 through 246 removed outlier: 3.638A pdb=" N LEU F 243 " --> pdb=" O PRO F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.760A pdb=" N ASN G 29 " --> pdb=" O GLN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 47 through 66 removed outlier: 3.676A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY G 53 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 60 - end of helix Processing helix chain 'G' and resid 68 through 84 removed outlier: 3.748A pdb=" N ALA G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 113 removed outlier: 3.796A pdb=" N ALA G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 124 removed outlier: 3.640A pdb=" N GLU G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 14 Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 98 through 117 removed outlier: 3.846A pdb=" N GLN H 103 " --> pdb=" O GLN H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 132 removed outlier: 3.554A pdb=" N VAL H 127 " --> pdb=" O GLY H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 removed outlier: 3.699A pdb=" N MET H 141 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN H 142 " --> pdb=" O SER H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 152 removed outlier: 3.809A pdb=" N CYS H 149 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 183 removed outlier: 3.532A pdb=" N GLU H 177 " --> pdb=" O LYS H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 258 removed outlier: 4.809A pdb=" N GLU H 249 " --> pdb=" O GLN H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 Processing helix chain 'H' and resid 301 through 314 removed outlier: 4.314A pdb=" N TYR H 312 " --> pdb=" O TYR H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 351 Processing helix chain 'H' and resid 351 through 361 Processing helix chain 'H' and resid 376 through 382 Processing helix chain 'H' and resid 400 through 407 Processing helix chain 'H' and resid 412 through 427 removed outlier: 4.137A pdb=" N LEU H 416 " --> pdb=" O PRO H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 447 removed outlier: 3.664A pdb=" N LEU H 436 " --> pdb=" O GLY H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 486 Processing helix chain 'H' and resid 492 through 502 removed outlier: 6.115A pdb=" N GLY H 499 " --> pdb=" O ASP H 495 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER H 500 " --> pdb=" O ARG H 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 502 " --> pdb=" O PHE H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 523 removed outlier: 3.673A pdb=" N VAL H 508 " --> pdb=" O THR H 504 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY H 510 " --> pdb=" O ILE H 506 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR H 511 " --> pdb=" O ALA H 507 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG H 514 " --> pdb=" O GLY H 510 " (cutoff:3.500A) Proline residue: H 517 - end of helix Processing helix chain 'H' and resid 525 through 542 removed outlier: 4.250A pdb=" N HIS H 542 " --> pdb=" O GLN H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 570 removed outlier: 3.635A pdb=" N PHE H 570 " --> pdb=" O THR H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 581 Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.759A pdb=" N ASN I 29 " --> pdb=" O GLN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 47 through 66 removed outlier: 3.676A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 60 - end of helix Processing helix chain 'I' and resid 68 through 84 removed outlier: 3.748A pdb=" N ALA I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 113 removed outlier: 3.796A pdb=" N ALA I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 124 removed outlier: 3.639A pdb=" N GLU I 124 " --> pdb=" O ASN I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.760A pdb=" N ASN J 29 " --> pdb=" O GLN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 44 Processing helix chain 'J' and resid 47 through 66 removed outlier: 3.675A pdb=" N VAL J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY J 53 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Proline residue: J 60 - end of helix Processing helix chain 'J' and resid 68 through 84 removed outlier: 3.748A pdb=" N ALA J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 113 removed outlier: 3.796A pdb=" N ALA J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 124 removed outlier: 3.640A pdb=" N GLU J 124 " --> pdb=" O ASN J 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 27 removed outlier: 3.808A pdb=" N GLY M 27 " --> pdb=" O PRO M 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 24 through 27' Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.901A pdb=" N LEU M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 105 removed outlier: 3.651A pdb=" N ARG M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'M' and resid 185 through 193 removed outlier: 4.006A pdb=" N GLN M 191 " --> pdb=" O HIS M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 209 Processing helix chain 'M' and resid 239 through 246 Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 117 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179 removed outlier: 3.574A pdb=" N PHE A 13 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 10 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 226 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 12 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 222 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 220 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 280 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.937A pdb=" N ARG A 31 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 removed outlier: 3.583A pdb=" N PHE A 183 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 251 removed outlier: 3.563A pdb=" N GLN A 248 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 250 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 265 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 179 removed outlier: 3.574A pdb=" N PHE B 13 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 10 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 226 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 12 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN B 222 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN B 220 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 280 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.342A pdb=" N LEU B 29 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 31 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.583A pdb=" N PHE B 183 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 251 removed outlier: 3.566A pdb=" N GLN B 248 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 250 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 265 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 178 through 179 removed outlier: 3.574A pdb=" N PHE C 13 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL C 10 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU C 226 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 12 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN C 222 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN C 220 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 280 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 23 removed outlier: 4.433A pdb=" N LEU C 29 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 31 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.583A pdb=" N PHE C 183 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 247 through 251 removed outlier: 3.566A pdb=" N GLN C 248 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 250 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 265 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 178 through 179 removed outlier: 3.574A pdb=" N PHE D 13 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL D 10 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU D 226 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU D 12 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN D 222 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN D 220 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 280 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.390A pdb=" N LEU D 29 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG D 31 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 131 removed outlier: 3.583A pdb=" N PHE D 183 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 247 through 251 removed outlier: 3.565A pdb=" N GLN D 248 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL D 250 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 265 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 178 through 179 removed outlier: 3.574A pdb=" N PHE E 13 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL E 10 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU E 226 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 12 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN E 222 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN E 220 " --> pdb=" O GLN E 16 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG E 280 " --> pdb=" O VAL E 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 31 through 32 removed outlier: 3.937A pdb=" N ARG E 31 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.583A pdb=" N PHE E 183 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 247 through 251 removed outlier: 3.562A pdb=" N GLN E 248 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL E 250 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 265 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 178 through 179 removed outlier: 3.573A pdb=" N PHE F 13 " --> pdb=" O TYR F 178 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL F 10 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU F 226 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 12 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN F 222 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN F 220 " --> pdb=" O GLN F 16 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 280 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 31 through 32 removed outlier: 3.936A pdb=" N ARG F 31 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 129 through 131 removed outlier: 3.583A pdb=" N PHE F 183 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 247 through 251 removed outlier: 3.555A pdb=" N GLN F 248 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL F 250 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 265 " --> pdb=" O VAL F 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 25 through 30 Processing sheet with id=AC8, first strand: chain 'H' and resid 33 through 36 Processing sheet with id=AC9, first strand: chain 'H' and resid 263 through 265 removed outlier: 3.821A pdb=" N THR H 270 " --> pdb=" O LEU H 330 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU H 330 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU H 327 " --> pdb=" O TRP H 342 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP H 342 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY H 329 " --> pdb=" O ARG H 340 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 6 through 7 removed outlier: 3.770A pdb=" N ARG M 6 " --> pdb=" O HIS M 231 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU M 12 " --> pdb=" O ARG M 224 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU M 226 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL M 10 " --> pdb=" O LEU M 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 6 through 7 removed outlier: 3.770A pdb=" N ARG M 6 " --> pdb=" O HIS M 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 22 through 23 removed outlier: 3.806A pdb=" N LEU M 29 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 247 through 251 removed outlier: 3.684A pdb=" N VAL M 250 " --> pdb=" O LEU M 265 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 23 through 24 removed outlier: 6.552A pdb=" N LYS N 96 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU N 11 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE N 4 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 62 through 64 removed outlier: 6.383A pdb=" N ASP N 105 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL N 51 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP N 107 " --> pdb=" O TRP N 49 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP N 49 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 69 through 70 807 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 8.70 Time building geometry restraints manager: 8.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8646 1.34 - 1.46: 4875 1.46 - 1.57: 14520 1.57 - 1.69: 268 1.69 - 1.81: 189 Bond restraints: 28498 Sorted by residual: bond pdb=" C1' A K 15 " pdb=" N9 A K 15 " ideal model delta sigma weight residual 1.465 1.484 -0.019 1.50e-02 4.44e+03 1.69e+00 bond pdb=" C3' G K 30 " pdb=" O3' G K 30 " ideal model delta sigma weight residual 1.427 1.410 0.017 1.50e-02 4.44e+03 1.33e+00 bond pdb=" C1' G K 4 " pdb=" N9 G K 4 " ideal model delta sigma weight residual 1.465 1.480 -0.015 1.50e-02 4.44e+03 1.05e+00 bond pdb=" C3' C K 21 " pdb=" O3' C K 21 " ideal model delta sigma weight residual 1.427 1.412 0.015 1.50e-02 4.44e+03 1.02e+00 bond pdb=" C3' U K 42 " pdb=" O3' U K 42 " ideal model delta sigma weight residual 1.427 1.412 0.015 1.50e-02 4.44e+03 9.91e-01 ... (remaining 28493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 38398 1.51 - 3.03: 550 3.03 - 4.54: 72 4.54 - 6.06: 22 6.06 - 7.57: 2 Bond angle restraints: 39044 Sorted by residual: angle pdb=" C3' G K 4 " pdb=" O3' G K 4 " pdb=" P A K 5 " ideal model delta sigma weight residual 120.20 125.66 -5.46 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P G K 10 " ideal model delta sigma weight residual 120.20 125.08 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" C ARG C 68 " pdb=" N GLU C 69 " pdb=" CA GLU C 69 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" O3' G K 4 " pdb=" C3' G K 4 " pdb=" C2' G K 4 " ideal model delta sigma weight residual 109.50 113.69 -4.19 1.50e+00 4.44e-01 7.81e+00 angle pdb=" C GLU D 90 " pdb=" N LYS D 91 " pdb=" CA LYS D 91 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.80e+00 ... (remaining 39039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 15886 35.87 - 71.74: 1032 71.74 - 107.60: 51 107.60 - 143.47: 3 143.47 - 179.34: 3 Dihedral angle restraints: 16975 sinusoidal: 8036 harmonic: 8939 Sorted by residual: dihedral pdb=" C4' C K 22 " pdb=" C3' C K 22 " pdb=" C2' C K 22 " pdb=" C1' C K 22 " ideal model delta sinusoidal sigma weight residual -35.00 31.00 -66.00 1 8.00e+00 1.56e-02 8.90e+01 dihedral pdb=" C5' C K 22 " pdb=" C4' C K 22 " pdb=" C3' C K 22 " pdb=" O3' C K 22 " ideal model delta sinusoidal sigma weight residual 147.00 83.58 63.42 1 8.00e+00 1.56e-02 8.29e+01 dihedral pdb=" O4' C K 22 " pdb=" C4' C K 22 " pdb=" C3' C K 22 " pdb=" C2' C K 22 " ideal model delta sinusoidal sigma weight residual 24.00 -32.67 56.67 1 8.00e+00 1.56e-02 6.76e+01 ... (remaining 16972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3639 0.050 - 0.100: 530 0.100 - 0.151: 74 0.151 - 0.201: 2 0.201 - 0.251: 4 Chirality restraints: 4249 Sorted by residual: chirality pdb=" C3' C K 22 " pdb=" C4' C K 22 " pdb=" O3' C K 22 " pdb=" C2' C K 22 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C2' C K 22 " pdb=" C3' C K 22 " pdb=" O2' C K 22 " pdb=" C1' C K 22 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4246 not shown) Planarity restraints: 4666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A K 6 " 0.031 2.00e-02 2.50e+03 1.38e-02 5.20e+00 pdb=" N9 A K 6 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A K 6 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A K 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A K 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A K 6 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A K 6 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A K 6 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A K 6 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C K 31 " 0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 C K 31 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C K 31 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C K 31 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C K 31 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C K 31 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C K 31 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C K 31 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C K 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 514 " -0.164 9.50e-02 1.11e+02 7.36e-02 3.43e+00 pdb=" NE ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 514 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 514 " -0.008 2.00e-02 2.50e+03 ... (remaining 4663 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 516 2.63 - 3.20: 23692 3.20 - 3.76: 47482 3.76 - 4.33: 65574 4.33 - 4.90: 104393 Nonbonded interactions: 241657 Sorted by model distance: nonbonded pdb=" N2 G K 30 " pdb=" O2 DC L 25 " model vdw 2.060 2.496 nonbonded pdb=" O THR A 148 " pdb=" O2' C K 31 " model vdw 2.135 3.040 nonbonded pdb=" O THR B 148 " pdb=" O2' U K 19 " model vdw 2.144 3.040 nonbonded pdb=" N2 G K 27 " pdb=" O2 DC L 28 " model vdw 2.161 2.496 nonbonded pdb=" O2 C K 43 " pdb=" N2 DG L 12 " model vdw 2.179 2.496 ... (remaining 241652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 72.070 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5153 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 : 0.002 0.039 28498 Z= 0.106 Angle : 0.448 7.574 39044 Z= 0.247 Chirality : 0.036 0.251 4249 Planarity : 0.003 0.074 4666 Dihedral : 20.282 179.338 11229 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 2.89 % Allowed : 13.63 % Favored : 83.48 % Rotamer: Outliers : 3.05 % Allowed : 20.50 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.13), residues: 3081 helix: -0.92 (0.15), residues: 1092 sheet: -3.81 (0.22), residues: 343 loop : -3.33 (0.12), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 203 HIS 0.001 0.000 HIS G 61 PHE 0.008 0.001 PHE N 192 TYR 0.013 0.001 TYR H 250 ARG 0.006 0.000 ARG H 514 Details of bonding type rmsd hydrogen bonds : bond 0.18318 ( 878) hydrogen bonds : angle 6.41266 ( 2455) covalent geometry : bond 0.00204 (28498) covalent geometry : angle 0.44770 (39044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1019 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.2211 (OUTLIER) cc_final: 0.1998 (m-80) REVERT: A 147 ILE cc_start: 0.6579 (pt) cc_final: 0.6377 (pt) REVERT: C 66 PHE cc_start: 0.2217 (OUTLIER) cc_final: 0.1562 (m-80) REVERT: C 150 MET cc_start: 0.5846 (ptm) cc_final: 0.5400 (ptm) REVERT: D 53 PHE cc_start: 0.1101 (t80) cc_final: 0.0764 (t80) REVERT: D 153 THR cc_start: 0.3888 (OUTLIER) cc_final: 0.3656 (m) REVERT: E 273 LEU cc_start: 0.3861 (pp) cc_final: 0.3339 (tp) REVERT: F 66 PHE cc_start: 0.3434 (OUTLIER) cc_final: 0.1847 (t80) REVERT: F 214 HIS cc_start: 0.4919 (m-70) cc_final: 0.4654 (m-70) REVERT: G 21 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7742 (mt) REVERT: H 48 THR cc_start: 0.6527 (p) cc_final: 0.6289 (p) REVERT: H 73 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6718 (mtmm) REVERT: H 141 MET cc_start: 0.7798 (mpp) cc_final: 0.7449 (mmm) REVERT: H 155 CYS cc_start: 0.4920 (t) cc_final: 0.4202 (t) REVERT: H 505 PRO cc_start: 0.6413 (Cg_exo) cc_final: 0.6067 (Cg_endo) REVERT: H 549 HIS cc_start: 0.6908 (t-90) cc_final: 0.6589 (t-90) REVERT: N 36 ASN cc_start: 0.2953 (m-40) cc_final: 0.2447 (m110) REVERT: N 83 ILE cc_start: 0.6968 (pt) cc_final: 0.6509 (pt) outliers start: 81 outliers final: 10 residues processed: 1072 average time/residue: 0.4928 time to fit residues: 803.7156 Evaluate side-chains 592 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 577 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 234 ASN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS E 62 HIS E 212 HIS ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN F 231 HIS ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 62 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 HIS H 41 ASN H 104 HIS H 156 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 ASN H 343 HIS ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN H 538 GLN H 548 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 ASN ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN M 181 HIS M 208 ASN N 61 GLN N 68 ASN N 88 GLN N 103 HIS N 133 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.151470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.133222 restraints weight = 68503.950| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 4.02 r_work: 0.4011 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 28498 Z= 0.306 Angle : 0.938 22.237 39044 Z= 0.479 Chirality : 0.052 0.261 4249 Planarity : 0.007 0.073 4666 Dihedral : 20.005 179.874 5160 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.58 % Favored : 89.03 % Rotamer: Outliers : 5.57 % Allowed : 22.54 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.13), residues: 3081 helix: -0.70 (0.15), residues: 1118 sheet: -3.05 (0.21), residues: 480 loop : -3.35 (0.13), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP J 77 HIS 0.012 0.002 HIS B 187 PHE 0.038 0.003 PHE G 52 TYR 0.047 0.003 TYR J 40 ARG 0.011 0.001 ARG N 143 Details of bonding type rmsd hydrogen bonds : bond 0.07116 ( 878) hydrogen bonds : angle 5.57528 ( 2455) covalent geometry : bond 0.00686 (28498) covalent geometry : angle 0.93796 (39044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 656 time to evaluate : 2.839 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: A 16 GLN cc_start: 0.7751 (mp10) cc_final: 0.6913 (mm-40) REVERT: A 21 ASN cc_start: 0.7918 (t0) cc_final: 0.7617 (t0) REVERT: A 63 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: A 139 PRO cc_start: 0.7023 (Cg_exo) cc_final: 0.6800 (Cg_endo) REVERT: A 141 MET cc_start: 0.7448 (mpp) cc_final: 0.6959 (mpp) REVERT: A 150 MET cc_start: 0.7305 (ptp) cc_final: 0.7087 (ptp) REVERT: A 220 GLN cc_start: 0.7252 (tt0) cc_final: 0.5967 (mt0) REVERT: B 4 GLU cc_start: 0.7787 (pm20) cc_final: 0.7312 (mp0) REVERT: B 7 TYR cc_start: 0.7965 (m-80) cc_final: 0.6881 (m-80) REVERT: B 143 LEU cc_start: 0.8587 (mt) cc_final: 0.8265 (mt) REVERT: B 161 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8034 (t) REVERT: B 166 THR cc_start: 0.7813 (m) cc_final: 0.7180 (p) REVERT: B 196 GLU cc_start: 0.7629 (tp30) cc_final: 0.6792 (tm-30) REVERT: B 230 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6798 (tp30) REVERT: B 273 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7131 (pp) REVERT: C 64 ASP cc_start: 0.4689 (OUTLIER) cc_final: 0.3993 (m-30) REVERT: C 93 GLU cc_start: 0.7194 (pm20) cc_final: 0.6540 (tm-30) REVERT: C 103 CYS cc_start: 0.5889 (OUTLIER) cc_final: 0.5434 (p) REVERT: C 150 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7684 (ptm) REVERT: C 166 THR cc_start: 0.7478 (p) cc_final: 0.7278 (p) REVERT: C 270 ASP cc_start: 0.6074 (p0) cc_final: 0.5850 (p0) REVERT: D 25 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6851 (t0) REVERT: D 93 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7897 (mm-30) REVERT: D 167 MET cc_start: 0.7745 (ttm) cc_final: 0.7457 (ttm) REVERT: D 221 MET cc_start: 0.7575 (mtm) cc_final: 0.7098 (mtp) REVERT: E 4 GLU cc_start: 0.7737 (pm20) cc_final: 0.7277 (pm20) REVERT: E 106 TYR cc_start: 0.6634 (m-80) cc_final: 0.6299 (t80) REVERT: E 166 THR cc_start: 0.4547 (OUTLIER) cc_final: 0.4345 (p) REVERT: E 204 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8365 (pp30) REVERT: E 209 MET cc_start: 0.6416 (ptp) cc_final: 0.5958 (ptm) REVERT: F 56 MET cc_start: 0.6581 (ptp) cc_final: 0.6204 (ptp) REVERT: F 66 PHE cc_start: 0.4241 (OUTLIER) cc_final: 0.2709 (t80) REVERT: F 116 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7341 (pmm) REVERT: F 204 GLN cc_start: 0.8969 (pt0) cc_final: 0.8655 (pp30) REVERT: G 25 GLN cc_start: 0.8622 (tt0) cc_final: 0.8285 (tt0) REVERT: H 29 GLU cc_start: 0.8541 (tt0) cc_final: 0.7780 (tp30) REVERT: H 80 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7254 (tp) REVERT: H 149 CYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6611 (p) REVERT: H 235 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6220 (tm-30) REVERT: H 344 GLU cc_start: 0.7489 (tt0) cc_final: 0.7130 (pm20) REVERT: I 12 TYR cc_start: 0.7495 (t80) cc_final: 0.6869 (t80) REVERT: I 68 PHE cc_start: 0.8519 (m-80) cc_final: 0.7452 (m-80) REVERT: I 91 ASN cc_start: 0.8098 (m110) cc_final: 0.7707 (m-40) REVERT: I 119 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7590 (mtmm) REVERT: M 53 PHE cc_start: 0.7997 (t80) cc_final: 0.7546 (t80) REVERT: M 64 ASP cc_start: 0.8220 (m-30) cc_final: 0.7823 (m-30) REVERT: M 106 TYR cc_start: 0.6673 (m-80) cc_final: 0.6472 (m-80) REVERT: M 178 TYR cc_start: 0.8830 (m-80) cc_final: 0.8257 (m-80) REVERT: M 247 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8188 (mt) REVERT: N 50 LYS cc_start: 0.7325 (pttm) cc_final: 0.6894 (pttm) REVERT: N 64 ASN cc_start: 0.7523 (p0) cc_final: 0.7015 (p0) REVERT: N 126 LYS cc_start: 0.8934 (tppt) cc_final: 0.8698 (tppt) REVERT: N 161 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.4738 (tt) outliers start: 148 outliers final: 57 residues processed: 745 average time/residue: 0.4308 time to fit residues: 494.6487 Evaluate side-chains 572 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 499 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 63 HIS Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 386 LEU Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 3 PHE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 35 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 231 HIS A 234 ASN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B 231 HIS C 81 HIS C 83 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 181 HIS ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN F 130 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 133 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.141536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.123829 restraints weight = 66838.610| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.79 r_work: 0.3882 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 28498 Z= 0.256 Angle : 0.784 16.138 39044 Z= 0.400 Chirality : 0.046 0.333 4249 Planarity : 0.005 0.073 4666 Dihedral : 19.882 177.062 5146 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.74 % Favored : 88.87 % Rotamer: Outliers : 5.72 % Allowed : 23.78 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.14), residues: 3081 helix: -0.32 (0.15), residues: 1118 sheet: -3.11 (0.20), residues: 489 loop : -3.18 (0.14), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 146 HIS 0.009 0.002 HIS A 187 PHE 0.027 0.002 PHE D 53 TYR 0.027 0.002 TYR N 26 ARG 0.013 0.001 ARG N 101 Details of bonding type rmsd hydrogen bonds : bond 0.05977 ( 878) hydrogen bonds : angle 5.27727 ( 2455) covalent geometry : bond 0.00570 (28498) covalent geometry : angle 0.78439 (39044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 575 time to evaluate : 3.075 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 8 ASP cc_start: 0.6961 (m-30) cc_final: 0.6597 (m-30) REVERT: A 64 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.6266 (m-30) REVERT: A 75 ASN cc_start: 0.7156 (m-40) cc_final: 0.6953 (t0) REVERT: A 141 MET cc_start: 0.7719 (mpp) cc_final: 0.7383 (mpp) REVERT: A 150 MET cc_start: 0.7687 (ptp) cc_final: 0.7289 (ptp) REVERT: A 183 PHE cc_start: 0.8599 (m-80) cc_final: 0.8324 (m-80) REVERT: A 184 ILE cc_start: 0.7643 (mm) cc_final: 0.7372 (mm) REVERT: A 199 LEU cc_start: 0.7537 (tp) cc_final: 0.7195 (tp) REVERT: A 248 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7085 (mp10) REVERT: B 7 TYR cc_start: 0.8450 (m-80) cc_final: 0.7075 (m-80) REVERT: B 29 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8519 (pp) REVERT: B 64 ASP cc_start: 0.6019 (OUTLIER) cc_final: 0.5389 (m-30) REVERT: B 66 PHE cc_start: 0.3410 (OUTLIER) cc_final: 0.2903 (m-80) REVERT: B 79 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6500 (pp20) REVERT: B 90 GLU cc_start: 0.6847 (tp30) cc_final: 0.6447 (tm-30) REVERT: B 143 LEU cc_start: 0.8468 (mt) cc_final: 0.8034 (mt) REVERT: B 166 THR cc_start: 0.7817 (m) cc_final: 0.7509 (p) REVERT: B 230 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6569 (tp30) REVERT: C 21 ASN cc_start: 0.8201 (t0) cc_final: 0.7936 (m-40) REVERT: C 23 ASP cc_start: 0.7703 (t0) cc_final: 0.7279 (t0) REVERT: C 25 ASP cc_start: 0.7683 (m-30) cc_final: 0.6766 (m-30) REVERT: C 68 ARG cc_start: 0.7297 (ttm170) cc_final: 0.7035 (ttm-80) REVERT: C 93 GLU cc_start: 0.7353 (pm20) cc_final: 0.6581 (tm-30) REVERT: C 150 MET cc_start: 0.8253 (ptm) cc_final: 0.7981 (ptm) REVERT: C 166 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7501 (p) REVERT: C 243 LEU cc_start: 0.8402 (tp) cc_final: 0.8039 (tp) REVERT: C 246 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7004 (ttm110) REVERT: C 248 GLN cc_start: 0.7998 (mm110) cc_final: 0.7624 (mp10) REVERT: D 4 GLU cc_start: 0.7000 (pp20) cc_final: 0.6567 (pp20) REVERT: D 25 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6554 (t0) REVERT: D 141 MET cc_start: 0.7846 (mmt) cc_final: 0.7578 (mmt) REVERT: D 166 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7404 (p) REVERT: D 167 MET cc_start: 0.7741 (ttm) cc_final: 0.7513 (ttm) REVERT: D 221 MET cc_start: 0.7966 (mtm) cc_final: 0.7707 (mtp) REVERT: D 271 LYS cc_start: 0.7798 (pttm) cc_final: 0.7574 (pttm) REVERT: E 41 VAL cc_start: 0.7881 (t) cc_final: 0.7577 (p) REVERT: E 66 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.3604 (m-10) REVERT: E 107 TYR cc_start: 0.6450 (t80) cc_final: 0.6123 (t80) REVERT: E 163 ASP cc_start: 0.3470 (OUTLIER) cc_final: 0.3107 (p0) REVERT: E 166 THR cc_start: 0.5414 (OUTLIER) cc_final: 0.5109 (p) REVERT: E 169 ARG cc_start: 0.7352 (mtp85) cc_final: 0.7121 (mmm160) REVERT: E 204 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8083 (pp30) REVERT: E 235 LEU cc_start: 0.5750 (OUTLIER) cc_final: 0.5418 (tt) REVERT: E 271 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5493 (ptpt) REVERT: F 53 PHE cc_start: 0.7789 (t80) cc_final: 0.7146 (t80) REVERT: F 66 PHE cc_start: 0.4008 (OUTLIER) cc_final: 0.2843 (t80) REVERT: F 116 MET cc_start: 0.7424 (mpp) cc_final: 0.7149 (mpp) REVERT: F 166 THR cc_start: 0.5257 (OUTLIER) cc_final: 0.5038 (p) REVERT: F 204 GLN cc_start: 0.8926 (pt0) cc_final: 0.8549 (tm-30) REVERT: G 68 PHE cc_start: 0.6563 (m-80) cc_final: 0.6324 (m-80) REVERT: G 77 TRP cc_start: 0.6802 (t60) cc_final: 0.6344 (t60) REVERT: H 29 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: H 215 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8007 (m-40) REVERT: H 235 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6580 (tm-30) REVERT: I 88 ARG cc_start: 0.8490 (tmt170) cc_final: 0.8227 (tmt170) REVERT: I 91 ASN cc_start: 0.8232 (m110) cc_final: 0.7812 (m-40) REVERT: I 108 GLU cc_start: 0.7772 (tp30) cc_final: 0.7195 (tp30) REVERT: I 119 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8147 (mtmm) REVERT: J 77 TRP cc_start: 0.7071 (t60) cc_final: 0.6835 (t60) REVERT: J 120 ASN cc_start: 0.8053 (m-40) cc_final: 0.7236 (m-40) REVERT: M 56 MET cc_start: 0.8159 (mtm) cc_final: 0.7542 (mtm) REVERT: M 64 ASP cc_start: 0.8186 (m-30) cc_final: 0.7787 (m-30) REVERT: M 109 ILE cc_start: 0.8951 (mm) cc_final: 0.8746 (mm) REVERT: M 150 MET cc_start: 0.8275 (mtp) cc_final: 0.7559 (mtp) REVERT: M 178 TYR cc_start: 0.8803 (m-80) cc_final: 0.8025 (m-80) REVERT: M 280 ARG cc_start: 0.7827 (mmp-170) cc_final: 0.7434 (mmp-170) REVERT: N 81 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8151 (mm) REVERT: N 123 GLU cc_start: 0.8723 (tp30) cc_final: 0.7852 (tm-30) REVERT: N 124 MET cc_start: 0.8687 (ptp) cc_final: 0.8014 (ptp) REVERT: N 161 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.4954 (tt) REVERT: N 175 MET cc_start: 0.7786 (mpp) cc_final: 0.7296 (mpp) REVERT: N 193 TYR cc_start: 0.7990 (t80) cc_final: 0.7513 (t80) outliers start: 152 outliers final: 70 residues processed: 676 average time/residue: 0.4062 time to fit residues: 432.7698 Evaluate side-chains 588 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 497 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 0.9980 chunk 271 optimal weight: 0.9990 chunk 296 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 220 GLN D 220 GLN E 55 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN F 191 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN M 231 HIS N 64 ASN N 136 HIS ** N 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.137817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.119800 restraints weight = 66437.374| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.84 r_work: 0.3809 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28498 Z= 0.214 Angle : 0.739 15.335 39044 Z= 0.377 Chirality : 0.045 0.316 4249 Planarity : 0.005 0.053 4666 Dihedral : 19.870 176.692 5145 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.80 % Favored : 89.81 % Rotamer: Outliers : 5.30 % Allowed : 25.51 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.14), residues: 3081 helix: -0.32 (0.15), residues: 1130 sheet: -3.02 (0.20), residues: 513 loop : -3.09 (0.14), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 146 HIS 0.011 0.001 HIS F 212 PHE 0.027 0.002 PHE D 53 TYR 0.025 0.002 TYR F 107 ARG 0.023 0.001 ARG F 224 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 878) hydrogen bonds : angle 5.24081 ( 2455) covalent geometry : bond 0.00478 (28498) covalent geometry : angle 0.73864 (39044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 538 time to evaluate : 3.160 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 8 ASP cc_start: 0.7692 (m-30) cc_final: 0.7123 (m-30) REVERT: A 16 GLN cc_start: 0.7491 (mt0) cc_final: 0.7091 (mp10) REVERT: A 134 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 138 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.5463 (m-30) REVERT: A 141 MET cc_start: 0.7925 (mpp) cc_final: 0.7604 (mpp) REVERT: A 150 MET cc_start: 0.7785 (ptp) cc_final: 0.7480 (ptp) REVERT: A 199 LEU cc_start: 0.7710 (tp) cc_final: 0.7370 (tp) REVERT: A 248 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6997 (mp10) REVERT: B 29 LEU cc_start: 0.8609 (pp) cc_final: 0.8382 (pp) REVERT: B 64 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5118 (m-30) REVERT: B 66 PHE cc_start: 0.3677 (OUTLIER) cc_final: 0.3152 (m-80) REVERT: B 90 GLU cc_start: 0.7663 (tp30) cc_final: 0.6882 (tm-30) REVERT: B 143 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8229 (mt) REVERT: B 209 MET cc_start: 0.7808 (ptt) cc_final: 0.7606 (ptt) REVERT: B 211 ASP cc_start: 0.7582 (m-30) cc_final: 0.7016 (p0) REVERT: C 23 ASP cc_start: 0.7652 (t0) cc_final: 0.7307 (t0) REVERT: C 25 ASP cc_start: 0.7784 (m-30) cc_final: 0.7160 (m-30) REVERT: C 64 ASP cc_start: 0.5751 (OUTLIER) cc_final: 0.4703 (m-30) REVERT: C 93 GLU cc_start: 0.7461 (pm20) cc_final: 0.6822 (tm-30) REVERT: C 103 CYS cc_start: 0.8393 (m) cc_final: 0.7478 (p) REVERT: C 166 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7469 (p) REVERT: C 243 LEU cc_start: 0.8563 (tp) cc_final: 0.8161 (tp) REVERT: D 4 GLU cc_start: 0.7377 (pp20) cc_final: 0.7001 (pp20) REVERT: D 25 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6645 (t0) REVERT: D 66 PHE cc_start: 0.3618 (t80) cc_final: 0.2438 (t80) REVERT: D 77 ILE cc_start: 0.6878 (mm) cc_final: 0.6605 (mm) REVERT: D 116 MET cc_start: 0.7798 (mpp) cc_final: 0.7168 (mpp) REVERT: D 141 MET cc_start: 0.8000 (mmt) cc_final: 0.7505 (mmt) REVERT: D 166 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7062 (p) REVERT: D 167 MET cc_start: 0.7704 (ttm) cc_final: 0.7334 (ttm) REVERT: D 220 GLN cc_start: 0.7929 (tt0) cc_final: 0.7519 (tt0) REVERT: D 271 LYS cc_start: 0.8032 (pttm) cc_final: 0.7772 (pttm) REVERT: E 41 VAL cc_start: 0.8219 (t) cc_final: 0.7896 (p) REVERT: E 66 PHE cc_start: 0.4334 (OUTLIER) cc_final: 0.3379 (m-10) REVERT: E 90 GLU cc_start: 0.8174 (tp30) cc_final: 0.7961 (tp30) REVERT: E 94 LYS cc_start: 0.6913 (tttp) cc_final: 0.6124 (tmtt) REVERT: E 150 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.6098 (mpp) REVERT: E 163 ASP cc_start: 0.3531 (OUTLIER) cc_final: 0.3320 (p0) REVERT: E 166 THR cc_start: 0.4899 (OUTLIER) cc_final: 0.4627 (p) REVERT: E 169 ARG cc_start: 0.7139 (mtp85) cc_final: 0.6685 (mmm160) REVERT: E 271 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.6010 (ptpt) REVERT: F 53 PHE cc_start: 0.8063 (t80) cc_final: 0.7795 (t80) REVERT: F 56 MET cc_start: 0.6691 (ptp) cc_final: 0.6469 (ptp) REVERT: F 66 PHE cc_start: 0.4002 (OUTLIER) cc_final: 0.2665 (t80) REVERT: F 116 MET cc_start: 0.7680 (mpp) cc_final: 0.7461 (mpp) REVERT: F 204 GLN cc_start: 0.8987 (pt0) cc_final: 0.8601 (tm-30) REVERT: F 227 TYR cc_start: 0.4710 (m-80) cc_final: 0.4400 (m-80) REVERT: G 68 PHE cc_start: 0.6434 (m-80) cc_final: 0.6198 (m-80) REVERT: G 77 TRP cc_start: 0.6636 (t60) cc_final: 0.6217 (t60) REVERT: H 1 MET cc_start: 0.7241 (ptt) cc_final: 0.5746 (tpt) REVERT: H 26 GLU cc_start: 0.7908 (pt0) cc_final: 0.7688 (pt0) REVERT: H 29 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: H 80 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7228 (tp) REVERT: H 87 TYR cc_start: 0.6490 (m-80) cc_final: 0.6276 (m-80) REVERT: H 98 GLU cc_start: 0.8878 (pt0) cc_final: 0.8605 (pt0) REVERT: H 141 MET cc_start: 0.9093 (mmt) cc_final: 0.8869 (mmt) REVERT: H 171 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: H 215 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: H 235 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6779 (tm-30) REVERT: H 446 ARG cc_start: 0.8094 (ptp90) cc_final: 0.7603 (mtt90) REVERT: I 91 ASN cc_start: 0.8166 (m110) cc_final: 0.7822 (m-40) REVERT: I 98 GLN cc_start: 0.8487 (tp40) cc_final: 0.8111 (tp40) REVERT: M 56 MET cc_start: 0.8549 (mtm) cc_final: 0.7901 (mtm) REVERT: M 64 ASP cc_start: 0.8215 (m-30) cc_final: 0.7917 (m-30) REVERT: M 150 MET cc_start: 0.8302 (mtp) cc_final: 0.7729 (mtp) REVERT: M 167 MET cc_start: 0.8825 (tpp) cc_final: 0.8352 (mpp) REVERT: M 178 TYR cc_start: 0.9152 (m-80) cc_final: 0.8264 (m-80) REVERT: N 25 SER cc_start: 0.9102 (p) cc_final: 0.8598 (m) REVERT: N 26 TYR cc_start: 0.8457 (m-80) cc_final: 0.8023 (m-80) REVERT: N 36 ASN cc_start: 0.6453 (m-40) cc_final: 0.6104 (m-40) REVERT: N 81 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7946 (mm) REVERT: N 123 GLU cc_start: 0.9043 (tp30) cc_final: 0.8152 (tm-30) REVERT: N 125 PHE cc_start: 0.8333 (t80) cc_final: 0.7945 (t80) REVERT: N 136 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.4922 (t-170) REVERT: N 147 CYS cc_start: 0.6438 (m) cc_final: 0.5946 (m) REVERT: N 161 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.4862 (tt) REVERT: N 193 TYR cc_start: 0.8121 (t80) cc_final: 0.7593 (t80) outliers start: 141 outliers final: 70 residues processed: 634 average time/residue: 0.4046 time to fit residues: 409.9499 Evaluate side-chains 581 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 489 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 15 optimal weight: 0.4980 chunk 212 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 301 optimal weight: 0.2980 chunk 293 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 220 GLN E 208 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 HIS ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN N 136 HIS ** N 194 GLN ** 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 = 0.4204 r_free = 0.4204 target = 0.137010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.118521 restraints weight = 65986.776| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.85 r_work: 0.3791 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28498 Z= 0.186 Angle : 0.712 14.364 39044 Z= 0.364 Chirality : 0.044 0.275 4249 Planarity : 0.004 0.056 4666 Dihedral : 19.835 175.713 5145 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.57 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.22 % Favored : 89.39 % Rotamer: Outliers : 4.74 % Allowed : 26.37 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 3081 helix: -0.27 (0.15), residues: 1124 sheet: -3.07 (0.19), residues: 557 loop : -2.95 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 77 HIS 0.010 0.001 HIS F 187 PHE 0.041 0.002 PHE E 53 TYR 0.018 0.002 TYR J 106 ARG 0.007 0.001 ARG N 90 Details of bonding type rmsd hydrogen bonds : bond 0.05736 ( 878) hydrogen bonds : angle 5.25598 ( 2455) covalent geometry : bond 0.00426 (28498) covalent geometry : angle 0.71195 (39044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 525 time to evaluate : 3.200 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: A 16 GLN cc_start: 0.7479 (mt0) cc_final: 0.7163 (mp10) REVERT: A 64 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.6241 (m-30) REVERT: A 68 ARG cc_start: 0.6263 (ttt-90) cc_final: 0.5959 (tpt-90) REVERT: A 124 GLN cc_start: 0.4990 (mm-40) cc_final: 0.4789 (mt0) REVERT: A 125 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.7632 (m) REVERT: A 138 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.5655 (m-30) REVERT: A 141 MET cc_start: 0.7730 (mpp) cc_final: 0.7473 (mpp) REVERT: A 150 MET cc_start: 0.7756 (ptp) cc_final: 0.7368 (ptp) REVERT: A 199 LEU cc_start: 0.7780 (tp) cc_final: 0.7438 (tp) REVERT: B 64 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5240 (m-30) REVERT: B 66 PHE cc_start: 0.3650 (OUTLIER) cc_final: 0.2979 (m-80) REVERT: B 90 GLU cc_start: 0.7519 (tp30) cc_final: 0.6779 (tm-30) REVERT: B 143 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 206 LEU cc_start: 0.7567 (tp) cc_final: 0.6985 (tp) REVERT: B 211 ASP cc_start: 0.7669 (m-30) cc_final: 0.7155 (p0) REVERT: C 23 ASP cc_start: 0.7656 (t0) cc_final: 0.7321 (t0) REVERT: C 25 ASP cc_start: 0.7910 (m-30) cc_final: 0.7175 (m-30) REVERT: C 103 CYS cc_start: 0.8406 (m) cc_final: 0.7472 (p) REVERT: C 150 MET cc_start: 0.8400 (ptm) cc_final: 0.8092 (ptp) REVERT: C 166 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7552 (p) REVERT: C 243 LEU cc_start: 0.8418 (tp) cc_final: 0.8195 (tp) REVERT: D 23 ASP cc_start: 0.8060 (t0) cc_final: 0.7769 (t0) REVERT: D 66 PHE cc_start: 0.3838 (t80) cc_final: 0.2654 (t80) REVERT: D 141 MET cc_start: 0.7983 (mmt) cc_final: 0.7401 (mmt) REVERT: D 166 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7018 (p) REVERT: D 220 GLN cc_start: 0.7896 (tt0) cc_final: 0.7431 (tt0) REVERT: D 221 MET cc_start: 0.7983 (mtm) cc_final: 0.7778 (mtm) REVERT: E 17 ASP cc_start: 0.6611 (m-30) cc_final: 0.6386 (t0) REVERT: E 41 VAL cc_start: 0.8341 (t) cc_final: 0.7999 (p) REVERT: E 66 PHE cc_start: 0.4337 (OUTLIER) cc_final: 0.3409 (m-10) REVERT: E 90 GLU cc_start: 0.8313 (tp30) cc_final: 0.8085 (tp30) REVERT: E 94 LYS cc_start: 0.6972 (tttp) cc_final: 0.6270 (tmtt) REVERT: E 150 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.6084 (mpp) REVERT: E 163 ASP cc_start: 0.3294 (OUTLIER) cc_final: 0.2177 (p0) REVERT: E 166 THR cc_start: 0.4864 (OUTLIER) cc_final: 0.4601 (p) REVERT: E 169 ARG cc_start: 0.7304 (mtp85) cc_final: 0.6992 (mmm160) REVERT: E 206 LEU cc_start: 0.8542 (tp) cc_final: 0.7995 (mp) REVERT: E 271 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6121 (ptpt) REVERT: F 53 PHE cc_start: 0.8047 (t80) cc_final: 0.7793 (t80) REVERT: F 116 MET cc_start: 0.7710 (mpp) cc_final: 0.7477 (mpp) REVERT: F 204 GLN cc_start: 0.8876 (pt0) cc_final: 0.8487 (tm-30) REVERT: F 248 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6452 (mm-40) REVERT: G 56 MET cc_start: 0.8005 (mmt) cc_final: 0.7791 (mmt) REVERT: G 77 TRP cc_start: 0.7024 (t60) cc_final: 0.6635 (t60) REVERT: G 78 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7053 (tm-30) REVERT: G 83 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7369 (tt) REVERT: G 107 HIS cc_start: 0.7655 (m-70) cc_final: 0.6592 (m90) REVERT: H 1 MET cc_start: 0.7290 (ptt) cc_final: 0.6033 (tpp) REVERT: H 98 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: H 141 MET cc_start: 0.9081 (mmt) cc_final: 0.8831 (mmt) REVERT: H 148 GLU cc_start: 0.7682 (tp30) cc_final: 0.7134 (tp30) REVERT: H 215 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8122 (m-40) REVERT: H 235 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6890 (tm-30) REVERT: H 271 THR cc_start: 0.8980 (m) cc_final: 0.8318 (p) REVERT: H 446 ARG cc_start: 0.8164 (ptp90) cc_final: 0.7795 (ptp90) REVERT: H 579 PHE cc_start: 0.8149 (t80) cc_final: 0.7790 (t80) REVERT: I 66 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8840 (mm) REVERT: I 67 GLU cc_start: 0.9081 (pt0) cc_final: 0.8734 (pt0) REVERT: I 91 ASN cc_start: 0.8121 (m110) cc_final: 0.7828 (m-40) REVERT: I 108 GLU cc_start: 0.7973 (tp30) cc_final: 0.7280 (tp30) REVERT: I 119 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8448 (mtpp) REVERT: J 65 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8788 (mmmt) REVERT: J 74 GLN cc_start: 0.8443 (tt0) cc_final: 0.7667 (mp10) REVERT: J 91 ASN cc_start: 0.8659 (m-40) cc_final: 0.8302 (m-40) REVERT: M 56 MET cc_start: 0.8538 (mtm) cc_final: 0.7980 (mtm) REVERT: M 64 ASP cc_start: 0.8182 (m-30) cc_final: 0.7800 (m-30) REVERT: M 150 MET cc_start: 0.8381 (mtp) cc_final: 0.7726 (mtp) REVERT: M 167 MET cc_start: 0.8573 (tpp) cc_final: 0.8063 (tpp) REVERT: M 175 TYR cc_start: 0.8629 (t80) cc_final: 0.8240 (t80) REVERT: M 178 TYR cc_start: 0.9110 (m-80) cc_final: 0.8013 (m-80) REVERT: M 198 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: M 280 ARG cc_start: 0.7741 (mmp-170) cc_final: 0.7444 (mmp-170) REVERT: N 25 SER cc_start: 0.8967 (p) cc_final: 0.8694 (m) REVERT: N 36 ASN cc_start: 0.5929 (m-40) cc_final: 0.5407 (m-40) REVERT: N 69 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: N 74 MET cc_start: 0.5989 (mpp) cc_final: 0.5476 (mpp) REVERT: N 81 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7793 (tp) REVERT: N 123 GLU cc_start: 0.8914 (tp30) cc_final: 0.8200 (tm-30) REVERT: N 125 PHE cc_start: 0.8276 (t80) cc_final: 0.7915 (t80) REVERT: N 136 HIS cc_start: 0.6830 (OUTLIER) cc_final: 0.5529 (t-90) REVERT: N 147 CYS cc_start: 0.6101 (m) cc_final: 0.5712 (m) REVERT: N 161 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.4898 (tt) REVERT: N 175 MET cc_start: 0.7625 (mpp) cc_final: 0.7337 (mpp) REVERT: N 193 TYR cc_start: 0.8110 (t80) cc_final: 0.7648 (t80) outliers start: 126 outliers final: 75 residues processed: 608 average time/residue: 0.3903 time to fit residues: 378.7269 Evaluate side-chains 580 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 483 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 175 TYR Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 50 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 285 optimal weight: 0.5980 chunk 228 optimal weight: 0.0370 chunk 90 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 145 HIS C 220 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.137282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.118730 restraints weight = 66387.373| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.87 r_work: 0.3812 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28498 Z= 0.166 Angle : 0.701 13.169 39044 Z= 0.359 Chirality : 0.043 0.262 4249 Planarity : 0.004 0.054 4666 Dihedral : 19.781 175.018 5143 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.00 % Favored : 89.61 % Rotamer: Outliers : 4.25 % Allowed : 27.39 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.14), residues: 3081 helix: -0.23 (0.15), residues: 1122 sheet: -2.91 (0.19), residues: 540 loop : -2.89 (0.14), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 77 HIS 0.012 0.001 HIS N 136 PHE 0.031 0.002 PHE E 53 TYR 0.035 0.002 TYR N 26 ARG 0.006 0.001 ARG M 31 Details of bonding type rmsd hydrogen bonds : bond 0.05606 ( 878) hydrogen bonds : angle 5.20883 ( 2455) covalent geometry : bond 0.00377 (28498) covalent geometry : angle 0.70139 (39044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 534 time to evaluate : 2.967 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: A 16 GLN cc_start: 0.7725 (mt0) cc_final: 0.7348 (mp10) REVERT: A 64 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.5758 (m-30) REVERT: A 68 ARG cc_start: 0.5795 (ttt-90) cc_final: 0.5583 (tpt-90) REVERT: A 116 MET cc_start: 0.5309 (mtp) cc_final: 0.4837 (ttt) REVERT: A 141 MET cc_start: 0.7749 (mpp) cc_final: 0.7365 (mpp) REVERT: A 150 MET cc_start: 0.7786 (ptp) cc_final: 0.7334 (ptp) REVERT: A 199 LEU cc_start: 0.7753 (tp) cc_final: 0.7410 (tp) REVERT: A 245 LYS cc_start: 0.8571 (mttt) cc_final: 0.7973 (mmtt) REVERT: A 271 LYS cc_start: 0.8161 (pttt) cc_final: 0.7651 (ttmt) REVERT: B 33 ASP cc_start: 0.8092 (t0) cc_final: 0.7293 (t70) REVERT: B 64 ASP cc_start: 0.6068 (OUTLIER) cc_final: 0.5341 (m-30) REVERT: B 66 PHE cc_start: 0.3646 (OUTLIER) cc_final: 0.3028 (m-80) REVERT: B 90 GLU cc_start: 0.7467 (tp30) cc_final: 0.6821 (tm-30) REVERT: B 96 GLU cc_start: 0.7847 (tp30) cc_final: 0.7263 (tm-30) REVERT: B 209 MET cc_start: 0.7751 (ptt) cc_final: 0.7486 (ptt) REVERT: B 211 ASP cc_start: 0.7557 (m-30) cc_final: 0.6918 (p0) REVERT: B 230 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6489 (tp30) REVERT: C 17 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6507 (t0) REVERT: C 23 ASP cc_start: 0.7592 (t0) cc_final: 0.7265 (t0) REVERT: C 25 ASP cc_start: 0.7612 (m-30) cc_final: 0.6846 (m-30) REVERT: C 40 LEU cc_start: 0.8047 (tt) cc_final: 0.7843 (tp) REVERT: C 144 GLU cc_start: 0.8406 (tt0) cc_final: 0.8191 (tm-30) REVERT: C 150 MET cc_start: 0.8352 (ptm) cc_final: 0.7991 (ptp) REVERT: C 166 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7504 (p) REVERT: C 209 MET cc_start: 0.8050 (ptt) cc_final: 0.7746 (ttp) REVERT: C 243 LEU cc_start: 0.8423 (tp) cc_final: 0.8193 (tp) REVERT: D 23 ASP cc_start: 0.8089 (t0) cc_final: 0.7711 (t0) REVERT: D 25 ASP cc_start: 0.6905 (t0) cc_final: 0.6547 (t0) REVERT: D 66 PHE cc_start: 0.3786 (t80) cc_final: 0.2701 (t80) REVERT: D 106 TYR cc_start: 0.6926 (m-80) cc_final: 0.6379 (m-80) REVERT: D 141 MET cc_start: 0.7904 (mmt) cc_final: 0.7302 (mmt) REVERT: D 166 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6682 (p) REVERT: D 167 MET cc_start: 0.7968 (ttm) cc_final: 0.7336 (ttm) REVERT: D 214 HIS cc_start: 0.6740 (m170) cc_final: 0.6521 (m170) REVERT: D 220 GLN cc_start: 0.7769 (tt0) cc_final: 0.7354 (tt0) REVERT: D 221 MET cc_start: 0.8061 (mtm) cc_final: 0.7776 (mtm) REVERT: E 66 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.3745 (m-80) REVERT: E 90 GLU cc_start: 0.8255 (tp30) cc_final: 0.7969 (tp30) REVERT: E 94 LYS cc_start: 0.7072 (tttp) cc_final: 0.6431 (tmtt) REVERT: E 163 ASP cc_start: 0.3787 (OUTLIER) cc_final: 0.3347 (p0) REVERT: E 169 ARG cc_start: 0.7428 (mtp85) cc_final: 0.7089 (mmm160) REVERT: E 206 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8070 (mp) REVERT: E 271 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.5607 (mmtm) REVERT: F 53 PHE cc_start: 0.8100 (t80) cc_final: 0.7866 (t80) REVERT: F 116 MET cc_start: 0.7639 (mpp) cc_final: 0.7423 (mpp) REVERT: F 204 GLN cc_start: 0.8865 (pt0) cc_final: 0.8572 (tm-30) REVERT: F 248 GLN cc_start: 0.6863 (mm-40) cc_final: 0.6633 (mm110) REVERT: G 56 MET cc_start: 0.7949 (mmt) cc_final: 0.7735 (mmt) REVERT: G 78 GLU cc_start: 0.7521 (tm-30) cc_final: 0.6998 (tm-30) REVERT: H 1 MET cc_start: 0.7249 (ptt) cc_final: 0.6077 (tpp) REVERT: H 26 GLU cc_start: 0.8040 (pt0) cc_final: 0.7835 (pt0) REVERT: H 59 ARG cc_start: 0.7461 (mtp-110) cc_final: 0.6792 (mtp-110) REVERT: H 98 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: H 148 GLU cc_start: 0.7630 (tp30) cc_final: 0.7192 (tp30) REVERT: H 171 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: H 215 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8115 (m-40) REVERT: H 235 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6687 (tm-30) REVERT: H 271 THR cc_start: 0.8994 (m) cc_final: 0.8358 (p) REVERT: H 327 LEU cc_start: 0.8317 (tp) cc_final: 0.8067 (tp) REVERT: H 342 TRP cc_start: 0.8450 (t-100) cc_final: 0.8025 (t-100) REVERT: H 420 LEU cc_start: 0.9027 (mm) cc_final: 0.8794 (mp) REVERT: H 446 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7782 (ptp90) REVERT: H 579 PHE cc_start: 0.8084 (t80) cc_final: 0.7780 (t80) REVERT: I 66 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8810 (mm) REVERT: I 67 GLU cc_start: 0.9122 (pt0) cc_final: 0.8767 (pt0) REVERT: I 91 ASN cc_start: 0.8098 (m110) cc_final: 0.7794 (m-40) REVERT: I 98 GLN cc_start: 0.8472 (tp40) cc_final: 0.7941 (tp40) REVERT: I 119 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8528 (mtpp) REVERT: J 65 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8556 (mmmt) REVERT: J 74 GLN cc_start: 0.8339 (tt0) cc_final: 0.7530 (mt0) REVERT: M 53 PHE cc_start: 0.8154 (t80) cc_final: 0.7583 (t80) REVERT: M 56 MET cc_start: 0.8493 (mtm) cc_final: 0.7946 (mtm) REVERT: M 64 ASP cc_start: 0.8122 (m-30) cc_final: 0.7701 (m-30) REVERT: M 150 MET cc_start: 0.8469 (mtp) cc_final: 0.7970 (mtp) REVERT: M 167 MET cc_start: 0.8407 (tpp) cc_final: 0.7998 (tpp) REVERT: M 175 TYR cc_start: 0.8643 (t80) cc_final: 0.8208 (t80) REVERT: M 178 TYR cc_start: 0.9084 (m-80) cc_final: 0.7920 (m-80) REVERT: M 221 MET cc_start: 0.8850 (mmm) cc_final: 0.8646 (mmm) REVERT: N 36 ASN cc_start: 0.6098 (m-40) cc_final: 0.5869 (m-40) REVERT: N 39 MET cc_start: 0.6418 (ptp) cc_final: 0.6168 (ptp) REVERT: N 69 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: N 81 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7800 (tp) REVERT: N 123 GLU cc_start: 0.8937 (tp30) cc_final: 0.8253 (tm-30) REVERT: N 125 PHE cc_start: 0.8243 (t80) cc_final: 0.7900 (t80) REVERT: N 136 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.5043 (t70) REVERT: N 161 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.4793 (tt) REVERT: N 175 MET cc_start: 0.7738 (mpp) cc_final: 0.7334 (mpp) REVERT: N 193 TYR cc_start: 0.8033 (t80) cc_final: 0.7534 (t80) outliers start: 113 outliers final: 67 residues processed: 608 average time/residue: 0.4209 time to fit residues: 406.5465 Evaluate side-chains 580 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 494 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 541 GLU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 300 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 chunk 314 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN J 91 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS N 136 HIS ** N 194 GLN ** 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 = 0.4142 r_free = 0.4142 target = 0.132419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.113868 restraints weight = 65935.213| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.78 r_work: 0.3738 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28498 Z= 0.205 Angle : 0.725 13.513 39044 Z= 0.373 Chirality : 0.044 0.251 4249 Planarity : 0.005 0.089 4666 Dihedral : 19.792 174.977 5143 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.68 % Favored : 88.87 % Rotamer: Outliers : 4.29 % Allowed : 27.65 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.14), residues: 3081 helix: -0.14 (0.15), residues: 1114 sheet: -2.86 (0.20), residues: 540 loop : -2.78 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 146 HIS 0.010 0.001 HIS H 518 PHE 0.025 0.002 PHE C 112 TYR 0.024 0.002 TYR N 26 ARG 0.016 0.001 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 878) hydrogen bonds : angle 5.22670 ( 2455) covalent geometry : bond 0.00468 (28498) covalent geometry : angle 0.72535 (39044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 535 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8503 (mp0) REVERT: A 16 GLN cc_start: 0.7584 (mt0) cc_final: 0.6710 (mt0) REVERT: A 64 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.5723 (m-30) REVERT: A 141 MET cc_start: 0.7780 (mpp) cc_final: 0.7551 (mpp) REVERT: A 150 MET cc_start: 0.8064 (ptp) cc_final: 0.7553 (ptp) REVERT: A 178 TYR cc_start: 0.7644 (m-80) cc_final: 0.7352 (m-10) REVERT: A 199 LEU cc_start: 0.8072 (tp) cc_final: 0.7747 (tp) REVERT: A 220 GLN cc_start: 0.8135 (tt0) cc_final: 0.7722 (tt0) REVERT: A 245 LYS cc_start: 0.8477 (mttt) cc_final: 0.8203 (mmtt) REVERT: A 271 LYS cc_start: 0.8038 (pttt) cc_final: 0.7552 (ttmt) REVERT: B 4 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: B 33 ASP cc_start: 0.8537 (t0) cc_final: 0.7933 (t70) REVERT: B 66 PHE cc_start: 0.4334 (OUTLIER) cc_final: 0.3593 (m-80) REVERT: B 90 GLU cc_start: 0.7616 (tp30) cc_final: 0.7004 (tm-30) REVERT: B 141 MET cc_start: 0.7379 (mmt) cc_final: 0.6926 (mmt) REVERT: B 143 LEU cc_start: 0.8500 (mt) cc_final: 0.8045 (mm) REVERT: B 209 MET cc_start: 0.8024 (ptt) cc_final: 0.7503 (ptt) REVERT: B 211 ASP cc_start: 0.7698 (m-30) cc_final: 0.6977 (p0) REVERT: B 253 ASP cc_start: 0.7270 (p0) cc_final: 0.6940 (p0) REVERT: C 17 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6874 (t0) REVERT: C 23 ASP cc_start: 0.7519 (t0) cc_final: 0.7222 (t0) REVERT: C 103 CYS cc_start: 0.8561 (m) cc_final: 0.7750 (p) REVERT: C 144 GLU cc_start: 0.8551 (tt0) cc_final: 0.8202 (tm-30) REVERT: C 166 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7554 (p) REVERT: D 23 ASP cc_start: 0.7910 (t0) cc_final: 0.7595 (t0) REVERT: D 25 ASP cc_start: 0.6789 (t0) cc_final: 0.6534 (t0) REVERT: D 106 TYR cc_start: 0.6964 (m-80) cc_final: 0.6277 (m-80) REVERT: D 134 SER cc_start: 0.8878 (m) cc_final: 0.7942 (p) REVERT: D 141 MET cc_start: 0.7927 (mmt) cc_final: 0.7192 (mmt) REVERT: D 166 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.7038 (p) REVERT: D 214 HIS cc_start: 0.7245 (m170) cc_final: 0.7039 (m170) REVERT: D 220 GLN cc_start: 0.7848 (tt0) cc_final: 0.7543 (tt0) REVERT: D 221 MET cc_start: 0.8239 (mtm) cc_final: 0.7886 (mtp) REVERT: E 66 PHE cc_start: 0.4216 (OUTLIER) cc_final: 0.3834 (m-80) REVERT: E 90 GLU cc_start: 0.8453 (tp30) cc_final: 0.8201 (tp30) REVERT: E 94 LYS cc_start: 0.7273 (tttp) cc_final: 0.6666 (tmtt) REVERT: E 102 MET cc_start: 0.8451 (tmm) cc_final: 0.8246 (tmm) REVERT: E 145 HIS cc_start: 0.8225 (m170) cc_final: 0.7959 (m170) REVERT: E 163 ASP cc_start: 0.4058 (OUTLIER) cc_final: 0.3390 (p0) REVERT: E 169 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7318 (mmm160) REVERT: E 206 LEU cc_start: 0.8577 (tp) cc_final: 0.8090 (mp) REVERT: E 271 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6045 (mmtm) REVERT: F 53 PHE cc_start: 0.8071 (t80) cc_final: 0.7575 (t80) REVERT: F 100 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8321 (mm110) REVERT: F 116 MET cc_start: 0.7827 (mpp) cc_final: 0.7607 (mpp) REVERT: F 141 MET cc_start: 0.0382 (ptp) cc_final: 0.0118 (ptt) REVERT: F 167 MET cc_start: 0.5792 (ptp) cc_final: 0.5405 (ptt) REVERT: F 204 GLN cc_start: 0.8896 (pt0) cc_final: 0.8692 (tm-30) REVERT: F 248 GLN cc_start: 0.6893 (mm-40) cc_final: 0.6593 (mm110) REVERT: G 52 PHE cc_start: 0.7412 (m-80) cc_final: 0.7124 (m-80) REVERT: G 78 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7325 (tm-30) REVERT: G 98 GLN cc_start: 0.7685 (mt0) cc_final: 0.7362 (mt0) REVERT: G 107 HIS cc_start: 0.7726 (m-70) cc_final: 0.6730 (m90) REVERT: H 1 MET cc_start: 0.7216 (ptt) cc_final: 0.6102 (tpt) REVERT: H 26 GLU cc_start: 0.8030 (pt0) cc_final: 0.7777 (pt0) REVERT: H 59 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.6957 (mtp-110) REVERT: H 98 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: H 148 GLU cc_start: 0.7634 (tp30) cc_final: 0.7201 (tp30) REVERT: H 171 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: H 215 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8229 (m-40) REVERT: H 235 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6929 (tm-30) REVERT: H 271 THR cc_start: 0.9016 (m) cc_final: 0.8470 (p) REVERT: H 327 LEU cc_start: 0.8346 (tp) cc_final: 0.8145 (tp) REVERT: H 342 TRP cc_start: 0.8524 (t-100) cc_final: 0.8137 (t-100) REVERT: H 446 ARG cc_start: 0.8229 (ptp90) cc_final: 0.7873 (ptp-170) REVERT: H 579 PHE cc_start: 0.8061 (t80) cc_final: 0.7797 (t80) REVERT: I 38 ASP cc_start: 0.8478 (m-30) cc_final: 0.7644 (m-30) REVERT: I 41 PHE cc_start: 0.9248 (t80) cc_final: 0.9033 (t80) REVERT: I 65 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8577 (tppt) REVERT: I 66 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8829 (mm) REVERT: I 67 GLU cc_start: 0.9109 (pt0) cc_final: 0.8759 (pt0) REVERT: I 91 ASN cc_start: 0.8222 (m110) cc_final: 0.7959 (m-40) REVERT: I 98 GLN cc_start: 0.8524 (tp40) cc_final: 0.8140 (tp-100) REVERT: J 65 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8650 (mmmt) REVERT: J 74 GLN cc_start: 0.8392 (tt0) cc_final: 0.7638 (mt0) REVERT: J 88 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8846 (ttt-90) REVERT: M 53 PHE cc_start: 0.8167 (t80) cc_final: 0.7500 (t80) REVERT: M 56 MET cc_start: 0.8584 (mtm) cc_final: 0.8276 (mtm) REVERT: M 64 ASP cc_start: 0.8178 (m-30) cc_final: 0.7733 (m-30) REVERT: M 116 MET cc_start: 0.8251 (mmp) cc_final: 0.7242 (tpt) REVERT: M 150 MET cc_start: 0.8375 (mtp) cc_final: 0.7769 (mtt) REVERT: M 167 MET cc_start: 0.8399 (tpp) cc_final: 0.7961 (tpp) REVERT: M 175 TYR cc_start: 0.8701 (t80) cc_final: 0.8398 (t80) REVERT: M 178 TYR cc_start: 0.9143 (m-80) cc_final: 0.7984 (m-80) REVERT: M 209 MET cc_start: 0.8913 (ptt) cc_final: 0.8478 (ttp) REVERT: M 221 MET cc_start: 0.8972 (mmm) cc_final: 0.8672 (mmm) REVERT: N 36 ASN cc_start: 0.6220 (m-40) cc_final: 0.5997 (m-40) REVERT: N 39 MET cc_start: 0.6473 (ptp) cc_final: 0.6143 (ptp) REVERT: N 69 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: N 74 MET cc_start: 0.6327 (mpt) cc_final: 0.5437 (mpp) REVERT: N 81 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7989 (tp) REVERT: N 123 GLU cc_start: 0.8862 (tp30) cc_final: 0.8243 (tm-30) REVERT: N 125 PHE cc_start: 0.8296 (t80) cc_final: 0.7916 (t80) REVERT: N 136 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5015 (t-170) REVERT: N 147 CYS cc_start: 0.5927 (m) cc_final: 0.5512 (m) REVERT: N 161 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.4990 (tt) REVERT: N 175 MET cc_start: 0.7544 (mpp) cc_final: 0.7291 (mpp) REVERT: N 193 TYR cc_start: 0.8023 (t80) cc_final: 0.7538 (t80) outliers start: 114 outliers final: 68 residues processed: 614 average time/residue: 0.4036 time to fit residues: 392.4810 Evaluate side-chains 580 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 494 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 541 GLU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 202 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 52 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 255 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN H 225 ASN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.133111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.114643 restraints weight = 66240.829| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.76 r_work: 0.3744 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.8386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28498 Z= 0.180 Angle : 0.725 15.886 39044 Z= 0.370 Chirality : 0.044 0.241 4249 Planarity : 0.005 0.061 4666 Dihedral : 19.759 173.756 5143 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.83 % Favored : 89.74 % Rotamer: Outliers : 3.99 % Allowed : 28.40 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.14), residues: 3081 helix: -0.24 (0.15), residues: 1117 sheet: -2.83 (0.20), residues: 550 loop : -2.76 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 146 HIS 0.015 0.001 HIS B 145 PHE 0.038 0.002 PHE E 53 TYR 0.022 0.002 TYR N 26 ARG 0.008 0.001 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.05608 ( 878) hydrogen bonds : angle 5.24261 ( 2455) covalent geometry : bond 0.00416 (28498) covalent geometry : angle 0.72514 (39044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 523 time to evaluate : 3.375 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 4 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8505 (mp0) REVERT: A 16 GLN cc_start: 0.7621 (mt0) cc_final: 0.6721 (mt0) REVERT: A 64 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.5780 (m-30) REVERT: A 116 MET cc_start: 0.5889 (mtp) cc_final: 0.5658 (ttt) REVERT: A 130 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7482 (mm-40) REVERT: A 141 MET cc_start: 0.7734 (mpp) cc_final: 0.7488 (mpp) REVERT: A 150 MET cc_start: 0.7943 (ptp) cc_final: 0.7413 (ptp) REVERT: A 178 TYR cc_start: 0.7665 (m-80) cc_final: 0.7362 (m-10) REVERT: A 220 GLN cc_start: 0.8252 (tt0) cc_final: 0.7877 (tt0) REVERT: A 245 LYS cc_start: 0.8538 (mttt) cc_final: 0.8218 (mmtt) REVERT: A 271 LYS cc_start: 0.8061 (pttt) cc_final: 0.7564 (ttmt) REVERT: B 4 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: B 33 ASP cc_start: 0.8540 (t0) cc_final: 0.7931 (t70) REVERT: B 63 HIS cc_start: 0.8153 (m-70) cc_final: 0.7848 (m90) REVERT: B 66 PHE cc_start: 0.4516 (OUTLIER) cc_final: 0.3780 (m-80) REVERT: B 90 GLU cc_start: 0.7687 (tp30) cc_final: 0.7075 (tm-30) REVERT: B 141 MET cc_start: 0.7487 (mmt) cc_final: 0.7058 (tpp) REVERT: B 209 MET cc_start: 0.7964 (ptt) cc_final: 0.7378 (ptt) REVERT: B 211 ASP cc_start: 0.7777 (m-30) cc_final: 0.6996 (p0) REVERT: B 230 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6600 (tp30) REVERT: C 23 ASP cc_start: 0.7446 (t0) cc_final: 0.7242 (t0) REVERT: C 144 GLU cc_start: 0.8487 (tt0) cc_final: 0.8165 (tm-30) REVERT: C 166 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.7015 (p) REVERT: C 167 MET cc_start: 0.7336 (mtp) cc_final: 0.6720 (mtp) REVERT: C 209 MET cc_start: 0.8305 (ptt) cc_final: 0.7821 (ttp) REVERT: C 243 LEU cc_start: 0.8604 (tp) cc_final: 0.8369 (tp) REVERT: D 23 ASP cc_start: 0.7828 (t0) cc_final: 0.7521 (t0) REVERT: D 69 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: D 90 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6915 (tm-30) REVERT: D 106 TYR cc_start: 0.6973 (m-80) cc_final: 0.6293 (m-80) REVERT: D 126 ARG cc_start: 0.8025 (tpt170) cc_final: 0.7758 (tpp80) REVERT: D 134 SER cc_start: 0.8955 (m) cc_final: 0.7967 (p) REVERT: D 141 MET cc_start: 0.7850 (mmt) cc_final: 0.7205 (mmt) REVERT: D 166 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6905 (p) REVERT: D 167 MET cc_start: 0.8160 (ttm) cc_final: 0.7742 (ttm) REVERT: D 209 MET cc_start: 0.8100 (tpp) cc_final: 0.7822 (tpt) REVERT: D 214 HIS cc_start: 0.7025 (m170) cc_final: 0.6812 (m170) REVERT: D 220 GLN cc_start: 0.7821 (tt0) cc_final: 0.7546 (tt0) REVERT: D 221 MET cc_start: 0.8112 (mtm) cc_final: 0.7780 (mtp) REVERT: E 21 ASN cc_start: 0.8413 (t0) cc_final: 0.7707 (t0) REVERT: E 66 PHE cc_start: 0.4344 (OUTLIER) cc_final: 0.3839 (m-80) REVERT: E 77 ILE cc_start: 0.6111 (mm) cc_final: 0.5871 (mm) REVERT: E 90 GLU cc_start: 0.8448 (tp30) cc_final: 0.8201 (tp30) REVERT: E 94 LYS cc_start: 0.7318 (tttp) cc_final: 0.6711 (tmtt) REVERT: E 143 LEU cc_start: 0.8014 (mt) cc_final: 0.7253 (mt) REVERT: E 145 HIS cc_start: 0.8104 (m170) cc_final: 0.7711 (m170) REVERT: E 163 ASP cc_start: 0.4233 (OUTLIER) cc_final: 0.3483 (p0) REVERT: E 206 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7984 (mp) REVERT: E 211 ASP cc_start: 0.7965 (m-30) cc_final: 0.7762 (m-30) REVERT: E 271 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6070 (mmtm) REVERT: F 53 PHE cc_start: 0.8042 (t80) cc_final: 0.7703 (t80) REVERT: F 96 GLU cc_start: 0.8268 (tp30) cc_final: 0.7332 (tp30) REVERT: F 100 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8267 (mm110) REVERT: F 116 MET cc_start: 0.7817 (mpp) cc_final: 0.7608 (mpp) REVERT: F 141 MET cc_start: 0.0314 (ptp) cc_final: 0.0065 (ptt) REVERT: F 167 MET cc_start: 0.5754 (ptp) cc_final: 0.5399 (ptt) REVERT: F 204 GLN cc_start: 0.8873 (pt0) cc_final: 0.8508 (tm-30) REVERT: F 212 HIS cc_start: 0.6033 (p-80) cc_final: 0.5762 (p90) REVERT: G 5 ARG cc_start: 0.7456 (mtm180) cc_final: 0.7000 (mtt-85) REVERT: G 52 PHE cc_start: 0.7273 (m-80) cc_final: 0.7050 (m-80) REVERT: G 56 MET cc_start: 0.7819 (mmt) cc_final: 0.7581 (mmt) REVERT: G 68 PHE cc_start: 0.5728 (m-80) cc_final: 0.5399 (m-80) REVERT: G 98 GLN cc_start: 0.7731 (mt0) cc_final: 0.7377 (mt0) REVERT: G 107 HIS cc_start: 0.7627 (m-70) cc_final: 0.6736 (m90) REVERT: H 1 MET cc_start: 0.7035 (ptt) cc_final: 0.5829 (tpt) REVERT: H 26 GLU cc_start: 0.8018 (pt0) cc_final: 0.7680 (pt0) REVERT: H 59 ARG cc_start: 0.7528 (mtp-110) cc_final: 0.7037 (mtp-110) REVERT: H 98 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: H 148 GLU cc_start: 0.7749 (tp30) cc_final: 0.7416 (tp30) REVERT: H 171 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: H 215 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8127 (m-40) REVERT: H 235 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6919 (tm-30) REVERT: H 248 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7293 (t80) REVERT: H 271 THR cc_start: 0.9059 (m) cc_final: 0.8683 (p) REVERT: H 327 LEU cc_start: 0.8370 (tp) cc_final: 0.8167 (tp) REVERT: H 342 TRP cc_start: 0.8542 (t-100) cc_final: 0.8208 (t-100) REVERT: H 579 PHE cc_start: 0.8029 (t80) cc_final: 0.7692 (t80) REVERT: I 27 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8672 (mm-30) REVERT: I 66 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8756 (mm) REVERT: I 67 GLU cc_start: 0.9105 (pt0) cc_final: 0.8830 (pt0) REVERT: I 88 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7630 (tmt170) REVERT: I 91 ASN cc_start: 0.8159 (m110) cc_final: 0.7495 (m-40) REVERT: I 98 GLN cc_start: 0.8577 (tp40) cc_final: 0.8337 (tp-100) REVERT: J 74 GLN cc_start: 0.8375 (tt0) cc_final: 0.7628 (mt0) REVERT: J 87 GLN cc_start: 0.8966 (tp40) cc_final: 0.8669 (tp40) REVERT: M 31 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6381 (ptp-170) REVERT: M 53 PHE cc_start: 0.8102 (t80) cc_final: 0.7430 (t80) REVERT: M 56 MET cc_start: 0.8634 (mtm) cc_final: 0.8291 (mtm) REVERT: M 116 MET cc_start: 0.8130 (mmp) cc_final: 0.7141 (tpt) REVERT: M 150 MET cc_start: 0.8281 (mtp) cc_final: 0.7661 (mtt) REVERT: M 167 MET cc_start: 0.8272 (tpp) cc_final: 0.7975 (tpp) REVERT: M 175 TYR cc_start: 0.8683 (t80) cc_final: 0.8429 (t80) REVERT: M 178 TYR cc_start: 0.9132 (m-80) cc_final: 0.7888 (m-80) REVERT: M 209 MET cc_start: 0.8902 (ptt) cc_final: 0.8490 (ttp) REVERT: M 221 MET cc_start: 0.8816 (mmm) cc_final: 0.8559 (mmm) REVERT: M 269 ASP cc_start: 0.8531 (m-30) cc_final: 0.8303 (m-30) REVERT: N 36 ASN cc_start: 0.6174 (m-40) cc_final: 0.5948 (m-40) REVERT: N 39 MET cc_start: 0.6420 (ptp) cc_final: 0.6052 (ptp) REVERT: N 69 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: N 74 MET cc_start: 0.6376 (mpt) cc_final: 0.5466 (mpp) REVERT: N 81 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7998 (tp) REVERT: N 123 GLU cc_start: 0.8854 (tp30) cc_final: 0.8277 (tm-30) REVERT: N 125 PHE cc_start: 0.8299 (t80) cc_final: 0.7967 (t80) REVERT: N 147 CYS cc_start: 0.5964 (m) cc_final: 0.5608 (m) REVERT: N 161 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.4835 (tt) REVERT: N 193 TYR cc_start: 0.7966 (t80) cc_final: 0.7314 (t80) outliers start: 106 outliers final: 69 residues processed: 597 average time/residue: 0.4166 time to fit residues: 399.2642 Evaluate side-chains 586 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 497 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 248 PHE Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 541 GLU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 117 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 GLN H 542 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.121737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102975 restraints weight = 66220.088| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.59 r_work: 0.3553 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.9466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 28498 Z= 0.306 Angle : 0.858 18.465 39044 Z= 0.434 Chirality : 0.048 0.262 4249 Planarity : 0.005 0.074 4666 Dihedral : 19.958 174.324 5143 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 31.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.17 % Favored : 88.41 % Rotamer: Outliers : 4.14 % Allowed : 28.59 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.14), residues: 3081 helix: -0.62 (0.15), residues: 1127 sheet: -2.84 (0.20), residues: 518 loop : -2.82 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 146 HIS 0.013 0.002 HIS B 145 PHE 0.022 0.003 PHE C 112 TYR 0.026 0.003 TYR G 106 ARG 0.012 0.001 ARG E 169 Details of bonding type rmsd hydrogen bonds : bond 0.06306 ( 878) hydrogen bonds : angle 5.60887 ( 2455) covalent geometry : bond 0.00691 (28498) covalent geometry : angle 0.85816 (39044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 526 time to evaluate : 3.461 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: A 4 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8535 (mp0) REVERT: A 16 GLN cc_start: 0.7510 (mt0) cc_final: 0.6826 (mp10) REVERT: A 64 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: A 116 MET cc_start: 0.6329 (mtp) cc_final: 0.5858 (mtp) REVERT: A 134 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8599 (p) REVERT: A 141 MET cc_start: 0.7778 (mpp) cc_final: 0.7568 (mpp) REVERT: A 144 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 248 GLN cc_start: 0.6971 (mp10) cc_final: 0.6627 (mp10) REVERT: A 271 LYS cc_start: 0.8543 (pttt) cc_final: 0.8014 (ptmm) REVERT: B 4 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: B 33 ASP cc_start: 0.8617 (t0) cc_final: 0.8103 (t70) REVERT: B 66 PHE cc_start: 0.4910 (OUTLIER) cc_final: 0.4236 (m-10) REVERT: B 90 GLU cc_start: 0.7978 (tp30) cc_final: 0.7185 (tm-30) REVERT: B 141 MET cc_start: 0.7848 (mmt) cc_final: 0.7474 (mmt) REVERT: B 209 MET cc_start: 0.8259 (ptt) cc_final: 0.7860 (ptt) REVERT: B 259 ARG cc_start: 0.7790 (mmp80) cc_final: 0.7468 (mmp80) REVERT: C 8 ASP cc_start: 0.8837 (m-30) cc_final: 0.8562 (m-30) REVERT: C 23 ASP cc_start: 0.7592 (t0) cc_final: 0.7251 (t0) REVERT: C 25 ASP cc_start: 0.8156 (m-30) cc_final: 0.7470 (m-30) REVERT: C 102 MET cc_start: 0.8171 (ttp) cc_final: 0.7775 (ppp) REVERT: C 103 CYS cc_start: 0.8562 (m) cc_final: 0.8319 (p) REVERT: C 116 MET cc_start: 0.8180 (mpp) cc_final: 0.7398 (mpp) REVERT: C 144 GLU cc_start: 0.8539 (tt0) cc_final: 0.8269 (tm-30) REVERT: C 166 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7427 (p) REVERT: C 167 MET cc_start: 0.7465 (mtp) cc_final: 0.6911 (mtp) REVERT: C 243 LEU cc_start: 0.8781 (tp) cc_final: 0.8557 (tp) REVERT: D 68 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7864 (tmm-80) REVERT: D 90 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 106 TYR cc_start: 0.7336 (m-80) cc_final: 0.6985 (m-80) REVERT: D 126 ARG cc_start: 0.7859 (tpt170) cc_final: 0.7644 (tpp80) REVERT: D 141 MET cc_start: 0.7973 (mmt) cc_final: 0.7296 (mmt) REVERT: D 166 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.7046 (p) REVERT: D 167 MET cc_start: 0.8223 (ttm) cc_final: 0.7607 (ttm) REVERT: D 209 MET cc_start: 0.8335 (tpp) cc_final: 0.7704 (tpt) REVERT: D 221 MET cc_start: 0.8499 (mtm) cc_final: 0.8155 (mtp) REVERT: E 21 ASN cc_start: 0.8221 (t0) cc_final: 0.7708 (t0) REVERT: E 66 PHE cc_start: 0.4882 (OUTLIER) cc_final: 0.4280 (m-80) REVERT: E 90 GLU cc_start: 0.8527 (tp30) cc_final: 0.7813 (tm-30) REVERT: E 94 LYS cc_start: 0.7765 (tttp) cc_final: 0.7217 (tmtt) REVERT: E 145 HIS cc_start: 0.8064 (m170) cc_final: 0.7654 (m170) REVERT: E 206 LEU cc_start: 0.8978 (tp) cc_final: 0.8536 (mp) REVERT: E 264 TYR cc_start: 0.2716 (OUTLIER) cc_final: 0.2086 (m-10) REVERT: F 53 PHE cc_start: 0.8316 (t80) cc_final: 0.7633 (t80) REVERT: F 96 GLU cc_start: 0.8164 (tp30) cc_final: 0.7163 (tp30) REVERT: F 100 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7918 (mm110) REVERT: F 116 MET cc_start: 0.8016 (mpp) cc_final: 0.7730 (mpp) REVERT: F 204 GLN cc_start: 0.8838 (pt0) cc_final: 0.8613 (tm-30) REVERT: F 209 MET cc_start: 0.7095 (mtm) cc_final: 0.6797 (pmm) REVERT: F 212 HIS cc_start: 0.6298 (p-80) cc_final: 0.6078 (p-80) REVERT: G 56 MET cc_start: 0.7956 (mmt) cc_final: 0.7713 (mmt) REVERT: G 74 GLN cc_start: 0.6353 (pm20) cc_final: 0.5963 (pm20) REVERT: H 1 MET cc_start: 0.7346 (ptt) cc_final: 0.6086 (tpt) REVERT: H 26 GLU cc_start: 0.7923 (pt0) cc_final: 0.7693 (pt0) REVERT: H 47 ASP cc_start: 0.7906 (p0) cc_final: 0.7474 (p0) REVERT: H 59 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.7112 (mtp-110) REVERT: H 98 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: H 148 GLU cc_start: 0.7694 (tp30) cc_final: 0.7273 (tp30) REVERT: H 171 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: H 215 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8636 (m-40) REVERT: H 235 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7044 (tm-30) REVERT: H 248 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7551 (t80) REVERT: H 277 LYS cc_start: 0.8894 (tppp) cc_final: 0.8423 (tppt) REVERT: H 342 TRP cc_start: 0.8734 (t-100) cc_final: 0.8466 (t-100) REVERT: H 393 LEU cc_start: 0.8628 (mp) cc_final: 0.8367 (mp) REVERT: H 579 PHE cc_start: 0.8129 (t80) cc_final: 0.7863 (t80) REVERT: I 66 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8810 (mm) REVERT: I 67 GLU cc_start: 0.9014 (pt0) cc_final: 0.8777 (pt0) REVERT: I 68 PHE cc_start: 0.8339 (m-80) cc_final: 0.8000 (m-80) REVERT: I 84 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8354 (tp30) REVERT: I 88 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7581 (tmt170) REVERT: I 91 ASN cc_start: 0.8290 (m110) cc_final: 0.7646 (m-40) REVERT: I 108 GLU cc_start: 0.8143 (tp30) cc_final: 0.7748 (tp30) REVERT: J 74 GLN cc_start: 0.8706 (tt0) cc_final: 0.8023 (mt0) REVERT: J 82 ILE cc_start: 0.8552 (mt) cc_final: 0.8069 (mt) REVERT: J 115 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7794 (mttm) REVERT: J 119 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8057 (mtpp) REVERT: M 56 MET cc_start: 0.8873 (mtm) cc_final: 0.8446 (mtm) REVERT: M 150 MET cc_start: 0.8552 (mtp) cc_final: 0.8177 (mtp) REVERT: M 167 MET cc_start: 0.8696 (tpp) cc_final: 0.8199 (tpp) REVERT: M 178 TYR cc_start: 0.9249 (m-80) cc_final: 0.7860 (m-80) REVERT: M 221 MET cc_start: 0.8952 (mmm) cc_final: 0.8608 (mmm) REVERT: N 36 ASN cc_start: 0.6481 (m-40) cc_final: 0.6268 (m-40) REVERT: N 69 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: N 74 MET cc_start: 0.7070 (mpt) cc_final: 0.5795 (mpp) REVERT: N 81 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8492 (mm) REVERT: N 97 ASP cc_start: 0.8259 (m-30) cc_final: 0.7817 (t70) REVERT: N 123 GLU cc_start: 0.8886 (tp30) cc_final: 0.8297 (tm-30) REVERT: N 124 MET cc_start: 0.8927 (ptp) cc_final: 0.7994 (ptp) REVERT: N 125 PHE cc_start: 0.8527 (t80) cc_final: 0.8106 (t80) REVERT: N 136 HIS cc_start: 0.6750 (OUTLIER) cc_final: 0.4878 (t70) REVERT: N 147 CYS cc_start: 0.5894 (m) cc_final: 0.5650 (m) REVERT: N 161 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5609 (mp) REVERT: N 175 MET cc_start: 0.8005 (mpp) cc_final: 0.7662 (mmt) REVERT: N 193 TYR cc_start: 0.8180 (t80) cc_final: 0.7670 (t80) outliers start: 110 outliers final: 68 residues processed: 599 average time/residue: 0.4969 time to fit residues: 467.4890 Evaluate side-chains 567 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 479 time to evaluate : 5.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 85 TYR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 248 PHE Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 305 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 238 optimal weight: 0.5980 chunk 242 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN B 208 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN D 55 GLN D 58 GLN D 62 HIS ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN H 417 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN J 120 ASN M 19 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.125167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106853 restraints weight = 66367.664| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.61 r_work: 0.3626 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.9567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28498 Z= 0.199 Angle : 0.792 15.898 39044 Z= 0.399 Chirality : 0.045 0.231 4249 Planarity : 0.005 0.066 4666 Dihedral : 19.906 172.874 5143 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.70 % Favored : 89.91 % Rotamer: Outliers : 3.54 % Allowed : 29.65 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.14), residues: 3081 helix: -0.62 (0.15), residues: 1125 sheet: -2.85 (0.20), residues: 531 loop : -2.80 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP H 146 HIS 0.013 0.002 HIS D 214 PHE 0.033 0.002 PHE A 53 TYR 0.033 0.002 TYR M 175 ARG 0.022 0.001 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.05818 ( 878) hydrogen bonds : angle 5.46834 ( 2455) covalent geometry : bond 0.00460 (28498) covalent geometry : angle 0.79154 (39044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 528 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8448 (mp0) REVERT: A 16 GLN cc_start: 0.7613 (mt0) cc_final: 0.7166 (mp10) REVERT: A 134 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8673 (p) REVERT: A 141 MET cc_start: 0.7834 (mpp) cc_final: 0.7564 (mpp) REVERT: A 145 HIS cc_start: 0.7989 (m170) cc_final: 0.7461 (m170) REVERT: A 220 GLN cc_start: 0.8280 (tt0) cc_final: 0.7993 (tt0) REVERT: A 248 GLN cc_start: 0.6803 (mp10) cc_final: 0.6479 (mp10) REVERT: A 271 LYS cc_start: 0.8558 (pttt) cc_final: 0.8035 (ptmm) REVERT: A 280 ARG cc_start: 0.8026 (ptp90) cc_final: 0.7810 (ptp90) REVERT: B 33 ASP cc_start: 0.8563 (t0) cc_final: 0.8010 (t70) REVERT: B 66 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.3067 (m-80) REVERT: B 90 GLU cc_start: 0.7841 (tp30) cc_final: 0.7070 (tm-30) REVERT: B 141 MET cc_start: 0.7758 (mmt) cc_final: 0.7497 (mmt) REVERT: B 209 MET cc_start: 0.8153 (ptt) cc_final: 0.7762 (ptt) REVERT: C 23 ASP cc_start: 0.7525 (t0) cc_final: 0.7217 (t0) REVERT: C 25 ASP cc_start: 0.8037 (m-30) cc_final: 0.7424 (m-30) REVERT: C 102 MET cc_start: 0.8227 (ttp) cc_final: 0.7580 (ppp) REVERT: C 103 CYS cc_start: 0.8466 (m) cc_final: 0.8243 (p) REVERT: C 116 MET cc_start: 0.8135 (mpp) cc_final: 0.7379 (mpp) REVERT: C 144 GLU cc_start: 0.8495 (tt0) cc_final: 0.8221 (tm-30) REVERT: C 167 MET cc_start: 0.7345 (mtp) cc_final: 0.6810 (mtp) REVERT: C 184 ILE cc_start: 0.8492 (mt) cc_final: 0.8236 (mt) REVERT: C 243 LEU cc_start: 0.8741 (tp) cc_final: 0.8511 (tp) REVERT: D 44 VAL cc_start: 0.7842 (m) cc_final: 0.7616 (m) REVERT: D 90 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7240 (tm-30) REVERT: D 106 TYR cc_start: 0.7171 (m-80) cc_final: 0.6683 (m-80) REVERT: D 141 MET cc_start: 0.7965 (mmt) cc_final: 0.7324 (mmt) REVERT: D 166 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6887 (p) REVERT: D 167 MET cc_start: 0.8371 (ttm) cc_final: 0.7944 (ttm) REVERT: D 209 MET cc_start: 0.8075 (tpp) cc_final: 0.7623 (tpt) REVERT: D 221 MET cc_start: 0.8219 (mtm) cc_final: 0.7939 (mtp) REVERT: D 280 ARG cc_start: 0.6635 (ptt90) cc_final: 0.6236 (ptm-80) REVERT: E 21 ASN cc_start: 0.7840 (t0) cc_final: 0.7554 (t0) REVERT: E 66 PHE cc_start: 0.4696 (OUTLIER) cc_final: 0.4202 (m-80) REVERT: E 90 GLU cc_start: 0.8502 (tp30) cc_final: 0.7666 (tm-30) REVERT: E 94 LYS cc_start: 0.7840 (tttp) cc_final: 0.7478 (tttp) REVERT: E 109 ILE cc_start: 0.9128 (mm) cc_final: 0.8759 (tt) REVERT: E 145 HIS cc_start: 0.8250 (m170) cc_final: 0.7729 (m170) REVERT: E 206 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 230 GLU cc_start: 0.6117 (mp0) cc_final: 0.5673 (mp0) REVERT: E 264 TYR cc_start: 0.2672 (OUTLIER) cc_final: 0.1958 (m-10) REVERT: F 53 PHE cc_start: 0.8220 (t80) cc_final: 0.7858 (t80) REVERT: F 96 GLU cc_start: 0.8206 (tp30) cc_final: 0.7250 (tp30) REVERT: F 100 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7872 (mm110) REVERT: F 116 MET cc_start: 0.7785 (mpp) cc_final: 0.7454 (mpp) REVERT: F 167 MET cc_start: 0.5907 (ptp) cc_final: 0.5498 (ptt) REVERT: F 204 GLN cc_start: 0.8862 (pt0) cc_final: 0.8522 (tm-30) REVERT: F 209 MET cc_start: 0.6660 (mtm) cc_final: 0.5970 (pmm) REVERT: G 68 PHE cc_start: 0.5779 (m-80) cc_final: 0.5249 (m-80) REVERT: G 98 GLN cc_start: 0.8114 (mt0) cc_final: 0.7842 (mt0) REVERT: G 107 HIS cc_start: 0.7585 (m-70) cc_final: 0.6442 (m90) REVERT: H 1 MET cc_start: 0.7298 (ptt) cc_final: 0.5904 (tpt) REVERT: H 26 GLU cc_start: 0.7995 (pt0) cc_final: 0.7773 (pt0) REVERT: H 47 ASP cc_start: 0.7628 (p0) cc_final: 0.7191 (p0) REVERT: H 59 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7108 (mtp-110) REVERT: H 98 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8162 (tp30) REVERT: H 148 GLU cc_start: 0.7730 (tp30) cc_final: 0.7417 (tp30) REVERT: H 171 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: H 215 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: H 235 GLU cc_start: 0.7527 (tm-30) cc_final: 0.6775 (tm-30) REVERT: H 248 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7615 (t80) REVERT: H 271 THR cc_start: 0.9074 (m) cc_final: 0.8547 (p) REVERT: H 277 LYS cc_start: 0.8856 (tppp) cc_final: 0.8481 (tppt) REVERT: H 342 TRP cc_start: 0.8629 (t-100) cc_final: 0.8346 (t-100) REVERT: H 579 PHE cc_start: 0.8041 (t80) cc_final: 0.7646 (t80) REVERT: I 27 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8753 (mm-30) REVERT: I 57 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8258 (mtm-85) REVERT: I 65 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8684 (tppt) REVERT: I 66 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8693 (mm) REVERT: I 67 GLU cc_start: 0.9061 (pt0) cc_final: 0.8760 (pt0) REVERT: I 68 PHE cc_start: 0.8360 (m-80) cc_final: 0.7992 (m-80) REVERT: I 84 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: I 88 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7502 (tmt170) REVERT: I 91 ASN cc_start: 0.8144 (m110) cc_final: 0.7536 (m-40) REVERT: I 108 GLU cc_start: 0.8325 (tp30) cc_final: 0.7972 (tp30) REVERT: J 74 GLN cc_start: 0.8582 (tt0) cc_final: 0.7997 (mt0) REVERT: J 88 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (ttt-90) REVERT: J 92 HIS cc_start: 0.8844 (t-90) cc_final: 0.8487 (t-170) REVERT: J 108 GLU cc_start: 0.7717 (tt0) cc_final: 0.7020 (tt0) REVERT: M 53 PHE cc_start: 0.8107 (t80) cc_final: 0.7461 (t80) REVERT: M 56 MET cc_start: 0.8768 (mtm) cc_final: 0.8411 (mtm) REVERT: M 116 MET cc_start: 0.8334 (mmp) cc_final: 0.7200 (tpt) REVERT: M 150 MET cc_start: 0.8361 (mtp) cc_final: 0.7742 (mtp) REVERT: M 167 MET cc_start: 0.8460 (tpp) cc_final: 0.8118 (tpp) REVERT: M 178 TYR cc_start: 0.9257 (m-80) cc_final: 0.7867 (m-80) REVERT: M 196 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8452 (mm-30) REVERT: M 221 MET cc_start: 0.8810 (mmm) cc_final: 0.8558 (mmm) REVERT: N 6 GLU cc_start: 0.8760 (tm-30) cc_final: 0.7963 (tm-30) REVERT: N 36 ASN cc_start: 0.6281 (m-40) cc_final: 0.6023 (m-40) REVERT: N 69 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: N 74 MET cc_start: 0.6593 (mpt) cc_final: 0.5596 (mpp) REVERT: N 81 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8419 (mm) REVERT: N 97 ASP cc_start: 0.8186 (m-30) cc_final: 0.7672 (t70) REVERT: N 123 GLU cc_start: 0.8721 (tp30) cc_final: 0.8293 (tm-30) REVERT: N 124 MET cc_start: 0.8898 (ptp) cc_final: 0.7935 (ptp) REVERT: N 125 PHE cc_start: 0.8375 (t80) cc_final: 0.8004 (t80) REVERT: N 136 HIS cc_start: 0.6380 (OUTLIER) cc_final: 0.4681 (t70) REVERT: N 147 CYS cc_start: 0.6313 (m) cc_final: 0.6081 (m) REVERT: N 161 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.4995 (tt) REVERT: N 193 TYR cc_start: 0.8154 (t80) cc_final: 0.7743 (t80) outliers start: 94 outliers final: 63 residues processed: 586 average time/residue: 0.4156 time to fit residues: 382.9332 Evaluate side-chains 568 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 487 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 248 PHE Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 90 ARG Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 172 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 272 optimal weight: 0.1980 chunk 241 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 208 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN E 212 HIS ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** 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 = 0.4064 r_free = 0.4064 target = 0.126606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109174 restraints weight = 65644.514| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.48 r_work: 0.3662 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.9577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28498 Z= 0.181 Angle : 0.775 16.021 39044 Z= 0.392 Chirality : 0.045 0.237 4249 Planarity : 0.005 0.072 4666 Dihedral : 19.883 174.898 5142 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.29 % Favored : 89.32 % Rotamer: Outliers : 3.39 % Allowed : 30.40 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.14), residues: 3081 helix: -0.57 (0.15), residues: 1124 sheet: -2.75 (0.20), residues: 525 loop : -2.82 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 146 HIS 0.012 0.001 HIS F 187 PHE 0.028 0.002 PHE D 53 TYR 0.027 0.002 TYR M 175 ARG 0.013 0.001 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.05678 ( 878) hydrogen bonds : angle 5.38233 ( 2455) covalent geometry : bond 0.00422 (28498) covalent geometry : angle 0.77533 (39044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14586.35 seconds wall clock time: 256 minutes 40.38 seconds (15400.38 seconds total)