Starting phenix.real_space_refine on Sun May 25 19:36:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gan_29901/05_2025/8gan_29901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gan_29901/05_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_29901/05_2025/8gan_29901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gan_29901/05_2025/8gan_29901.map" model { file = "/net/cci-nas-00/data/ceres_data/8gan_29901/05_2025/8gan_29901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gan_29901/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 15.18, per 1000 atoms: 0.55 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: 7.21 Conformation dependent library (CDL) restraints added in 3.7 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: 9.26 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: 9.43 Time building geometry restraints manager: 7.90 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: 1.710 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: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 65.350 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.460 ------------------------------------------------------------------------------- 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 : 2.822 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: 0.4447 time to fit residues: 717.1557 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 : 2.953 ------------------------------------------------------------------------------- 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** B 231 HIS 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.151621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.133100 restraints weight = 68780.295| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 4.05 r_work: 0.4010 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5083 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= 0.307 Angle : 0.937 22.197 39044 Z= 0.478 Chirality : 0.052 0.261 4249 Planarity : 0.007 0.073 4666 Dihedral : 20.005 179.875 5160 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 25.45 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.65 % Favored : 88.96 % Rotamer: Outliers : 5.61 % Allowed : 22.54 % Favored : 71.86 % 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 0.011 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 0.07113 ( 878) hydrogen bonds : angle 5.57465 ( 2455) covalent geometry : bond 0.00686 (28498) covalent geometry : angle 0.93741 (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 805 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 656 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.6912 (mm-40) REVERT: A 21 ASN cc_start: 0.7912 (t0) cc_final: 0.7614 (t0) REVERT: A 63 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: A 139 PRO cc_start: 0.7020 (Cg_exo) cc_final: 0.6798 (Cg_endo) REVERT: A 141 MET cc_start: 0.7438 (mpp) cc_final: 0.6952 (mpp) REVERT: A 150 MET cc_start: 0.7311 (ptp) cc_final: 0.7093 (ptp) REVERT: A 220 GLN cc_start: 0.7251 (tt0) cc_final: 0.5966 (mt0) REVERT: B 4 GLU cc_start: 0.7793 (pm20) cc_final: 0.7317 (mp0) REVERT: B 7 TYR cc_start: 0.7965 (m-80) cc_final: 0.6886 (m-80) REVERT: B 143 LEU cc_start: 0.8582 (mt) cc_final: 0.8261 (mt) REVERT: B 161 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8035 (t) REVERT: B 166 THR cc_start: 0.7817 (m) cc_final: 0.7185 (p) REVERT: B 196 GLU cc_start: 0.7619 (tp30) cc_final: 0.6784 (tm-30) REVERT: B 230 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6825 (tp30) REVERT: B 273 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7142 (pp) REVERT: C 64 ASP cc_start: 0.4696 (OUTLIER) cc_final: 0.4004 (m-30) REVERT: C 93 GLU cc_start: 0.7207 (pm20) cc_final: 0.6544 (tm-30) REVERT: C 103 CYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5423 (p) REVERT: C 150 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7674 (ptm) REVERT: C 166 THR cc_start: 0.7486 (p) cc_final: 0.7286 (p) REVERT: C 270 ASP cc_start: 0.6072 (p0) cc_final: 0.5850 (p0) REVERT: D 25 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6848 (t0) REVERT: D 93 GLU cc_start: 0.8643 (mt-10) cc_final: 0.7893 (mm-30) REVERT: D 167 MET cc_start: 0.7754 (ttm) cc_final: 0.7473 (ttm) REVERT: D 221 MET cc_start: 0.7574 (mtm) cc_final: 0.7102 (mtp) REVERT: E 4 GLU cc_start: 0.7741 (pm20) cc_final: 0.7278 (pm20) REVERT: E 106 TYR cc_start: 0.6634 (m-80) cc_final: 0.6299 (t80) REVERT: E 166 THR cc_start: 0.4541 (OUTLIER) cc_final: 0.4339 (p) REVERT: E 204 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8368 (pp30) REVERT: E 209 MET cc_start: 0.6421 (ptp) cc_final: 0.5965 (ptm) REVERT: F 56 MET cc_start: 0.6593 (ptp) cc_final: 0.6219 (ptp) REVERT: F 66 PHE cc_start: 0.4221 (OUTLIER) cc_final: 0.2694 (t80) REVERT: F 116 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7369 (pmm) REVERT: F 204 GLN cc_start: 0.8974 (pt0) cc_final: 0.8662 (pp30) REVERT: G 25 GLN cc_start: 0.8612 (tt0) cc_final: 0.8273 (tt0) REVERT: H 29 GLU cc_start: 0.8550 (tt0) cc_final: 0.7791 (tp30) REVERT: H 80 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7258 (tp) REVERT: H 149 CYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6593 (p) REVERT: H 235 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6232 (tm-30) REVERT: H 344 GLU cc_start: 0.7479 (tt0) cc_final: 0.7135 (pm20) REVERT: I 12 TYR cc_start: 0.7485 (t80) cc_final: 0.6862 (t80) REVERT: I 68 PHE cc_start: 0.8522 (m-80) cc_final: 0.7466 (m-80) REVERT: I 91 ASN cc_start: 0.8102 (m110) cc_final: 0.7718 (m-40) REVERT: I 119 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7602 (mtmm) REVERT: M 53 PHE cc_start: 0.7993 (t80) cc_final: 0.7543 (t80) REVERT: M 64 ASP cc_start: 0.8216 (m-30) cc_final: 0.7821 (m-30) REVERT: M 106 TYR cc_start: 0.6679 (m-80) cc_final: 0.6476 (m-80) REVERT: M 178 TYR cc_start: 0.8827 (m-80) cc_final: 0.8258 (m-80) REVERT: M 247 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8191 (mt) REVERT: N 50 LYS cc_start: 0.7344 (pttm) cc_final: 0.6916 (pttm) REVERT: N 64 ASN cc_start: 0.7516 (p0) cc_final: 0.7011 (p0) REVERT: N 126 LYS cc_start: 0.8929 (tppt) cc_final: 0.8697 (tppt) REVERT: N 161 LEU cc_start: 0.5966 (OUTLIER) cc_final: 0.4743 (tt) outliers start: 149 outliers final: 57 residues processed: 745 average time/residue: 0.4385 time to fit residues: 501.8803 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 : 2.795 ------------------------------------------------------------------------------- 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: 0.9990 chunk 246 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 236 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 145 HIS ** 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 C 81 HIS C 83 GLN C 220 GLN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 55 GLN E 181 HIS 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 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 ** 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 ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 89 GLN N 133 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.144306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.126678 restraints weight = 66935.287| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 3.81 r_work: 0.3928 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 28498 Z= 0.228 Angle : 0.759 16.440 39044 Z= 0.386 Chirality : 0.045 0.293 4249 Planarity : 0.005 0.060 4666 Dihedral : 19.841 176.912 5146 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.42 % Favored : 89.19 % Rotamer: Outliers : 5.64 % Allowed : 24.00 % Favored : 70.35 % 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: -3.10 (0.14), residues: 3081 helix: -0.32 (0.15), residues: 1117 sheet: -2.95 (0.21), residues: 470 loop : -3.19 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 146 HIS 0.014 0.002 HIS A 187 PHE 0.026 0.002 PHE D 53 TYR 0.022 0.002 TYR N 26 ARG 0.009 0.001 ARG M 31 Details of bonding type rmsd hydrogen bonds : bond 0.05974 ( 878) hydrogen bonds : angle 5.23217 ( 2455) covalent geometry : bond 0.00520 (28498) covalent geometry : angle 0.75940 (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 713 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 563 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7350 (mp10) cc_final: 0.7037 (mp10) REVERT: A 64 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6121 (m-30) REVERT: A 141 MET cc_start: 0.7654 (mpp) cc_final: 0.7285 (mpp) REVERT: A 150 MET cc_start: 0.7498 (ptp) cc_final: 0.7079 (ptp) REVERT: A 199 LEU cc_start: 0.7319 (tp) cc_final: 0.6988 (tp) REVERT: A 248 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6982 (mp10) REVERT: B 7 TYR cc_start: 0.8353 (m-80) cc_final: 0.7392 (m-80) REVERT: B 29 LEU cc_start: 0.8743 (pp) cc_final: 0.8494 (pp) REVERT: B 64 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5327 (m-30) REVERT: B 66 PHE cc_start: 0.2943 (OUTLIER) cc_final: 0.2219 (m-80) REVERT: B 79 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6321 (pp20) REVERT: B 90 GLU cc_start: 0.6698 (tp30) cc_final: 0.6375 (tm-30) REVERT: B 143 LEU cc_start: 0.8433 (mt) cc_final: 0.8011 (mt) REVERT: B 166 THR cc_start: 0.7828 (m) cc_final: 0.7413 (p) REVERT: C 23 ASP cc_start: 0.7656 (t0) cc_final: 0.7306 (t0) REVERT: C 64 ASP cc_start: 0.5103 (OUTLIER) cc_final: 0.4248 (m-30) REVERT: C 93 GLU cc_start: 0.7144 (pm20) cc_final: 0.6419 (tm-30) REVERT: C 150 MET cc_start: 0.8114 (ptm) cc_final: 0.7806 (ptm) REVERT: C 166 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7461 (p) REVERT: C 220 GLN cc_start: 0.7801 (tt0) cc_final: 0.7565 (tt0) REVERT: C 243 LEU cc_start: 0.8323 (tp) cc_final: 0.7994 (tp) REVERT: C 270 ASP cc_start: 0.6168 (p0) cc_final: 0.5867 (p0) REVERT: D 4 GLU cc_start: 0.6935 (pp20) cc_final: 0.6663 (pp20) REVERT: D 25 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6545 (t0) REVERT: D 141 MET cc_start: 0.7731 (mmt) cc_final: 0.7530 (mmt) REVERT: D 166 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7257 (p) REVERT: D 167 MET cc_start: 0.7714 (ttm) cc_final: 0.7449 (ttm) REVERT: D 221 MET cc_start: 0.7935 (mtm) cc_final: 0.7549 (mtp) REVERT: D 271 LYS cc_start: 0.7612 (pttm) cc_final: 0.7363 (pttm) REVERT: E 41 VAL cc_start: 0.7363 (t) cc_final: 0.7087 (p) REVERT: E 66 PHE cc_start: 0.4456 (OUTLIER) cc_final: 0.3621 (m-10) REVERT: E 107 TYR cc_start: 0.6352 (t80) cc_final: 0.6059 (t80) REVERT: E 163 ASP cc_start: 0.3264 (OUTLIER) cc_final: 0.2064 (p0) REVERT: E 165 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6981 (mtt180) REVERT: E 166 THR cc_start: 0.5299 (OUTLIER) cc_final: 0.5059 (p) REVERT: E 169 ARG cc_start: 0.7310 (mtp85) cc_final: 0.7056 (mmm160) REVERT: E 204 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8183 (pp30) REVERT: E 220 GLN cc_start: 0.7643 (tt0) cc_final: 0.7406 (tt0) REVERT: E 235 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4830 (tt) REVERT: E 271 LYS cc_start: 0.5848 (OUTLIER) cc_final: 0.5377 (ptpt) REVERT: F 53 PHE cc_start: 0.7778 (t80) cc_final: 0.7121 (t80) REVERT: F 66 PHE cc_start: 0.3866 (OUTLIER) cc_final: 0.2720 (t80) REVERT: F 116 MET cc_start: 0.7484 (mpp) cc_final: 0.7273 (mpp) REVERT: F 166 THR cc_start: 0.5239 (OUTLIER) cc_final: 0.5037 (p) REVERT: F 204 GLN cc_start: 0.8952 (pt0) cc_final: 0.8573 (tm-30) REVERT: G 68 PHE cc_start: 0.6531 (m-80) cc_final: 0.6293 (m-80) REVERT: G 77 TRP cc_start: 0.6770 (t60) cc_final: 0.6314 (t60) REVERT: H 215 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7906 (m-40) REVERT: H 235 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6066 (tm-30) REVERT: H 271 THR cc_start: 0.8855 (m) cc_final: 0.8378 (p) REVERT: I 12 TYR cc_start: 0.7460 (t80) cc_final: 0.6995 (t80) REVERT: I 88 ARG cc_start: 0.8411 (tmt170) cc_final: 0.8139 (tmt170) REVERT: I 91 ASN cc_start: 0.8169 (m110) cc_final: 0.7751 (m-40) REVERT: I 108 GLU cc_start: 0.7743 (tp30) cc_final: 0.7174 (tp30) REVERT: I 119 LYS cc_start: 0.8571 (mtmm) cc_final: 0.7963 (mtmm) REVERT: M 53 PHE cc_start: 0.8214 (t80) cc_final: 0.7654 (t80) REVERT: M 56 MET cc_start: 0.8092 (mtm) cc_final: 0.7505 (mtm) REVERT: M 64 ASP cc_start: 0.8149 (m-30) cc_final: 0.7641 (m-30) REVERT: M 109 ILE cc_start: 0.8841 (mm) cc_final: 0.8602 (mm) REVERT: M 150 MET cc_start: 0.8231 (mtp) cc_final: 0.7723 (mtm) REVERT: M 178 TYR cc_start: 0.8822 (m-80) cc_final: 0.8121 (m-80) REVERT: M 280 ARG cc_start: 0.7854 (mmp-170) cc_final: 0.7593 (mmp-170) REVERT: N 50 LYS cc_start: 0.7341 (pttm) cc_final: 0.6996 (ptpp) REVERT: N 54 ILE cc_start: 0.7926 (mp) cc_final: 0.7722 (mp) REVERT: N 123 GLU cc_start: 0.8796 (tp30) cc_final: 0.7966 (tm-30) REVERT: N 124 MET cc_start: 0.8605 (ptp) cc_final: 0.7983 (ptp) REVERT: N 161 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.4899 (tt) REVERT: N 175 MET cc_start: 0.7667 (mpp) cc_final: 0.7250 (mpp) REVERT: N 193 TYR cc_start: 0.8018 (t80) cc_final: 0.7552 (t80) outliers start: 150 outliers final: 71 residues processed: 668 average time/residue: 0.3882 time to fit residues: 407.4568 Evaluate side-chains 584 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 495 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL 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 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 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 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 64 ASP Chi-restraints excluded: chain C residue 109 ILE 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 255 VAL Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 156 LYS 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 75 TYR 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 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 I residue 98 GLN 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 44 VAL Chi-restraints excluded: chain M residue 108 ASP 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 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 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: 0.5980 chunk 296 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 142 optimal weight: 0.0010 chunk 171 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 222 ASN D 220 GLN E 55 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 233 ASN E 272 ASN F 191 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 490 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** 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 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 = 0.4285 r_free = 0.4285 target = 0.143075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.124698 restraints weight = 67011.833| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.98 r_work: 0.3892 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28498 Z= 0.176 Angle : 0.716 14.581 39044 Z= 0.365 Chirality : 0.044 0.280 4249 Planarity : 0.004 0.058 4666 Dihedral : 19.803 176.522 5144 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.70 % Favored : 89.91 % Rotamer: Outliers : 5.04 % Allowed : 25.55 % Favored : 69.41 % 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: -3.01 (0.14), residues: 3081 helix: -0.24 (0.15), residues: 1130 sheet: -3.13 (0.19), residues: 543 loop : -3.03 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP J 77 HIS 0.010 0.001 HIS F 212 PHE 0.026 0.002 PHE I 101 TYR 0.032 0.002 TYR M 175 ARG 0.006 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05765 ( 878) hydrogen bonds : angle 5.16039 ( 2455) covalent geometry : bond 0.00390 (28498) covalent geometry : angle 0.71614 (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 680 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 546 time to evaluate : 3.087 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: 0.7405 (mp10) cc_final: 0.6903 (mp10) REVERT: A 141 MET cc_start: 0.7570 (mpp) cc_final: 0.7136 (mpp) REVERT: A 150 MET cc_start: 0.7340 (ptp) cc_final: 0.7000 (ptp) REVERT: A 199 LEU cc_start: 0.7364 (tp) cc_final: 0.7041 (tp) REVERT: A 220 GLN cc_start: 0.7711 (tt0) cc_final: 0.7196 (tt0) REVERT: A 244 PHE cc_start: 0.7772 (m-10) cc_final: 0.7509 (m-10) REVERT: A 248 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6847 (mp10) REVERT: B 29 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8331 (pp) REVERT: B 64 ASP cc_start: 0.5870 (OUTLIER) cc_final: 0.5150 (m-30) REVERT: B 66 PHE cc_start: 0.2986 (OUTLIER) cc_final: 0.2733 (m-80) REVERT: B 90 GLU cc_start: 0.7202 (tp30) cc_final: 0.6659 (tm-30) REVERT: B 109 ILE cc_start: 0.8946 (mt) cc_final: 0.8541 (mt) REVERT: B 143 LEU cc_start: 0.8421 (mt) cc_final: 0.8190 (mt) REVERT: B 211 ASP cc_start: 0.7399 (m-30) cc_final: 0.6841 (p0) REVERT: C 15 VAL cc_start: 0.6618 (OUTLIER) cc_final: 0.6361 (t) REVERT: C 23 ASP cc_start: 0.7651 (t0) cc_final: 0.7260 (t0) REVERT: C 93 GLU cc_start: 0.7166 (pm20) cc_final: 0.6469 (tm-30) REVERT: C 103 CYS cc_start: 0.8299 (m) cc_final: 0.7906 (t) REVERT: C 134 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7511 (p) REVERT: C 166 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7405 (p) REVERT: C 270 ASP cc_start: 0.6645 (p0) cc_final: 0.6231 (p0) REVERT: C 280 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6993 (ptm160) REVERT: D 4 GLU cc_start: 0.7241 (pp20) cc_final: 0.6894 (pp20) REVERT: D 25 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6732 (t0) REVERT: D 67 ILE cc_start: 0.4812 (OUTLIER) cc_final: 0.4369 (mp) REVERT: D 106 TYR cc_start: 0.6497 (m-80) cc_final: 0.6066 (m-80) REVERT: D 125 VAL cc_start: 0.8032 (p) cc_final: 0.7830 (t) REVERT: D 141 MET cc_start: 0.8011 (mmt) cc_final: 0.7529 (mmt) REVERT: D 166 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.7021 (p) REVERT: D 167 MET cc_start: 0.7704 (ttm) cc_final: 0.7358 (ttm) REVERT: D 220 GLN cc_start: 0.7712 (tt0) cc_final: 0.7219 (tt0) REVERT: D 271 LYS cc_start: 0.7966 (pttm) cc_final: 0.7704 (pttm) REVERT: E 41 VAL cc_start: 0.7930 (t) cc_final: 0.7607 (p) REVERT: E 66 PHE cc_start: 0.4283 (OUTLIER) cc_final: 0.3347 (m-10) REVERT: E 150 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6101 (mpp) REVERT: E 163 ASP cc_start: 0.3353 (OUTLIER) cc_final: 0.3143 (p0) REVERT: E 166 THR cc_start: 0.4867 (OUTLIER) cc_final: 0.4600 (p) REVERT: E 169 ARG cc_start: 0.7202 (mtp85) cc_final: 0.6743 (mmm160) REVERT: E 204 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: E 235 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5245 (tt) REVERT: F 53 PHE cc_start: 0.8024 (t80) cc_final: 0.7568 (t80) REVERT: F 56 MET cc_start: 0.6589 (ptp) cc_final: 0.6359 (ptp) REVERT: F 66 PHE cc_start: 0.3512 (OUTLIER) cc_final: 0.2508 (t80) REVERT: F 116 MET cc_start: 0.7664 (mpp) cc_final: 0.7423 (mpp) REVERT: F 178 TYR cc_start: 0.6021 (m-80) cc_final: 0.5624 (m-80) REVERT: F 204 GLN cc_start: 0.8983 (pt0) cc_final: 0.8599 (tm-30) REVERT: F 214 HIS cc_start: 0.5561 (m90) cc_final: 0.5308 (m90) REVERT: F 227 TYR cc_start: 0.4546 (m-80) cc_final: 0.4134 (m-80) REVERT: G 68 PHE cc_start: 0.6405 (m-80) cc_final: 0.6184 (m-80) REVERT: G 77 TRP cc_start: 0.6614 (t60) cc_final: 0.6183 (t60) REVERT: H 1 MET cc_start: 0.7278 (ptt) cc_final: 0.6008 (tpt) REVERT: H 80 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7161 (tp) REVERT: H 87 TYR cc_start: 0.6366 (m-80) cc_final: 0.5969 (m-80) REVERT: H 141 MET cc_start: 0.9132 (mmt) cc_final: 0.8871 (mmt) REVERT: H 148 GLU cc_start: 0.7733 (tp30) cc_final: 0.7383 (tp30) REVERT: H 171 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: H 215 ASN cc_start: 0.8599 (m110) cc_final: 0.7889 (m-40) REVERT: H 235 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6116 (tm-30) REVERT: H 271 THR cc_start: 0.9037 (m) cc_final: 0.8436 (p) REVERT: I 91 ASN cc_start: 0.8084 (m110) cc_final: 0.7780 (m-40) REVERT: J 107 HIS cc_start: 0.8180 (m-70) cc_final: 0.7300 (m-70) REVERT: M 53 PHE cc_start: 0.8222 (t80) cc_final: 0.7617 (t80) REVERT: M 56 MET cc_start: 0.8320 (mtm) cc_final: 0.8113 (mtm) REVERT: M 66 PHE cc_start: 0.7260 (t80) cc_final: 0.6462 (t80) REVERT: M 116 MET cc_start: 0.8441 (mmt) cc_final: 0.7396 (tpp) REVERT: M 150 MET cc_start: 0.8443 (mtp) cc_final: 0.7592 (mtp) REVERT: M 167 MET cc_start: 0.8593 (tpp) cc_final: 0.8347 (tpp) REVERT: M 175 TYR cc_start: 0.8680 (t80) cc_final: 0.8203 (t80) REVERT: M 178 TYR cc_start: 0.9078 (m-80) cc_final: 0.8318 (m-80) REVERT: M 221 MET cc_start: 0.8732 (mtp) cc_final: 0.8368 (mmt) REVERT: M 280 ARG cc_start: 0.7763 (mmp-170) cc_final: 0.7343 (mmp-170) REVERT: N 26 TYR cc_start: 0.8343 (m-80) cc_final: 0.7513 (m-80) REVERT: N 68 ASN cc_start: 0.8156 (m-40) cc_final: 0.7951 (m110) REVERT: N 81 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7583 (mm) REVERT: N 123 GLU cc_start: 0.9022 (tp30) cc_final: 0.8219 (tm-30) REVERT: N 147 CYS cc_start: 0.6481 (m) cc_final: 0.5982 (m) REVERT: N 161 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.4731 (tt) REVERT: N 193 TYR cc_start: 0.8086 (t80) cc_final: 0.7699 (t80) outliers start: 134 outliers final: 67 residues processed: 630 average time/residue: 0.3959 time to fit residues: 393.7556 Evaluate side-chains 578 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 490 time to evaluate : 2.705 ------------------------------------------------------------------------------- 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 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 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 103 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 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 111 THR Chi-restraints excluded: chain C residue 134 SER 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 264 TYR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 67 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 77 ILE Chi-restraints excluded: chain E residue 100 GLN 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 204 GLN Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 235 LEU 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 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 80 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 171 GLN 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 I residue 100 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 67 GLU 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 108 ASP 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 15 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 229 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN ** 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 145 HIS C 220 GLN ** E 214 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 417 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN M 63 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.136537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.117993 restraints weight = 66161.648| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.85 r_work: 0.3792 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28498 Z= 0.224 Angle : 0.737 15.005 39044 Z= 0.375 Chirality : 0.044 0.291 4249 Planarity : 0.005 0.055 4666 Dihedral : 19.835 175.960 5144 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.55 % Favored : 89.03 % Rotamer: Outliers : 4.82 % Allowed : 26.22 % Favored : 68.96 % 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: -2.94 (0.14), residues: 3081 helix: -0.21 (0.15), residues: 1125 sheet: -3.01 (0.19), residues: 547 loop : -2.98 (0.14), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 77 HIS 0.014 0.001 HIS N 136 PHE 0.028 0.002 PHE N 135 TYR 0.022 0.002 TYR M 175 ARG 0.009 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05775 ( 878) hydrogen bonds : angle 5.25235 ( 2455) covalent geometry : bond 0.00512 (28498) covalent geometry : angle 0.73665 (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 637 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 509 time to evaluate : 2.799 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: 0.7429 (mp10) cc_final: 0.7035 (mt0) REVERT: A 64 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.6194 (m-30) REVERT: A 68 ARG cc_start: 0.6122 (ttt-90) cc_final: 0.5823 (tpt-90) REVERT: A 138 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.5677 (m-30) REVERT: A 141 MET cc_start: 0.7677 (mpp) cc_final: 0.7327 (mpp) REVERT: A 150 MET cc_start: 0.7936 (ptp) cc_final: 0.7602 (ptp) REVERT: A 199 LEU cc_start: 0.7746 (tp) cc_final: 0.7395 (tp) REVERT: A 248 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7197 (mp10) REVERT: B 29 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8448 (pp) REVERT: B 64 ASP cc_start: 0.6193 (OUTLIER) cc_final: 0.5488 (m-30) REVERT: B 66 PHE cc_start: 0.3761 (OUTLIER) cc_final: 0.3037 (m-80) REVERT: B 90 GLU cc_start: 0.7672 (tp30) cc_final: 0.6947 (tm-30) REVERT: B 143 LEU cc_start: 0.8660 (mt) cc_final: 0.8316 (mt) REVERT: B 211 ASP cc_start: 0.7565 (m-30) cc_final: 0.7052 (p0) REVERT: C 8 ASP cc_start: 0.8678 (m-30) cc_final: 0.8449 (m-30) REVERT: C 23 ASP cc_start: 0.7596 (t0) cc_final: 0.7201 (t0) REVERT: C 41 VAL cc_start: 0.8124 (t) cc_final: 0.7656 (t) REVERT: C 103 CYS cc_start: 0.8418 (m) cc_final: 0.7503 (p) REVERT: C 107 TYR cc_start: 0.7893 (t80) cc_final: 0.7481 (t80) REVERT: C 134 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7684 (p) REVERT: C 150 MET cc_start: 0.8205 (ptm) cc_final: 0.7940 (ptp) REVERT: C 166 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 177 LEU cc_start: 0.8083 (mp) cc_final: 0.7880 (mm) REVERT: C 245 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8532 (mmtm) REVERT: C 280 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7222 (ptm160) REVERT: D 25 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6685 (t0) REVERT: D 66 PHE cc_start: 0.3897 (t80) cc_final: 0.2745 (t80) REVERT: D 141 MET cc_start: 0.7991 (mmt) cc_final: 0.7457 (mmt) REVERT: D 166 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7106 (p) REVERT: D 167 MET cc_start: 0.7810 (ttm) cc_final: 0.7333 (ttm) REVERT: D 220 GLN cc_start: 0.7946 (tt0) cc_final: 0.7501 (tt0) REVERT: D 221 MET cc_start: 0.7903 (mtm) cc_final: 0.7596 (mtp) REVERT: D 271 LYS cc_start: 0.8100 (pttm) cc_final: 0.7844 (pttm) REVERT: E 66 PHE cc_start: 0.4368 (OUTLIER) cc_final: 0.3420 (m-10) REVERT: E 150 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6063 (mpp) REVERT: E 163 ASP cc_start: 0.3710 (OUTLIER) cc_final: 0.3328 (p0) REVERT: E 169 ARG cc_start: 0.7325 (mtp85) cc_final: 0.6959 (mmm160) REVERT: E 204 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: F 53 PHE cc_start: 0.7999 (t80) cc_final: 0.7684 (t80) REVERT: F 116 MET cc_start: 0.7701 (mpp) cc_final: 0.7484 (mpp) REVERT: F 178 TYR cc_start: 0.6389 (m-80) cc_final: 0.5982 (m-80) REVERT: F 204 GLN cc_start: 0.8878 (pt0) cc_final: 0.8582 (tm-30) REVERT: G 68 PHE cc_start: 0.6359 (m-80) cc_final: 0.6116 (m-80) REVERT: G 78 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7252 (tm-30) REVERT: G 107 HIS cc_start: 0.7561 (m-70) cc_final: 0.6559 (m90) REVERT: H 1 MET cc_start: 0.7291 (ptt) cc_final: 0.5997 (tpp) REVERT: H 141 MET cc_start: 0.9078 (mmt) cc_final: 0.8844 (mmt) REVERT: H 148 GLU cc_start: 0.7732 (tp30) cc_final: 0.7524 (tp30) REVERT: H 215 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: H 235 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6781 (tm-30) REVERT: H 271 THR cc_start: 0.9094 (m) cc_final: 0.8478 (p) REVERT: H 361 LEU cc_start: 0.9080 (tp) cc_final: 0.8877 (mt) REVERT: H 446 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7708 (ptp-170) REVERT: I 91 ASN cc_start: 0.8174 (m110) cc_final: 0.7887 (m-40) REVERT: I 119 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8473 (mtpp) REVERT: J 65 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8748 (mmmt) REVERT: J 84 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8568 (mm-30) REVERT: M 2 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7529 (m) REVERT: M 56 MET cc_start: 0.8533 (mtm) cc_final: 0.7824 (mtm) REVERT: M 66 PHE cc_start: 0.7699 (t80) cc_final: 0.7126 (t80) REVERT: M 150 MET cc_start: 0.8365 (mtp) cc_final: 0.7790 (mtp) REVERT: M 167 MET cc_start: 0.8593 (tpp) cc_final: 0.8299 (tpp) REVERT: M 178 TYR cc_start: 0.9133 (m-80) cc_final: 0.8094 (m-80) REVERT: N 36 ASN cc_start: 0.5751 (m-40) cc_final: 0.5393 (m-40) REVERT: N 64 ASN cc_start: 0.7879 (p0) cc_final: 0.7569 (p0) REVERT: N 69 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: N 81 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7838 (tp) REVERT: N 123 GLU cc_start: 0.8960 (tp30) cc_final: 0.8218 (tm-30) REVERT: N 147 CYS cc_start: 0.6213 (m) cc_final: 0.5875 (m) REVERT: N 161 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.4920 (tt) REVERT: N 175 MET cc_start: 0.7909 (mpp) cc_final: 0.7496 (mpp) REVERT: N 193 TYR cc_start: 0.8148 (t80) cc_final: 0.7758 (t80) outliers start: 128 outliers final: 73 residues processed: 597 average time/residue: 0.3836 time to fit residues: 363.5002 Evaluate side-chains 562 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 469 time to evaluate : 2.867 ------------------------------------------------------------------------------- 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 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 265 LEU Chi-restraints excluded: chain B residue 29 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 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 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 245 LYS Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 280 ARG 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 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 172 THR Chi-restraints excluded: chain E residue 204 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 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 17 LEU 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 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 257 LEU 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 411 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL 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 J residue 17 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 2 THR 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 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP 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 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: 4.9990 chunk 226 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 228 optimal weight: 0.0980 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 220 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 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 87 GLN J 120 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN N 136 HIS N 137 GLN ** 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 = 0.4210 r_free = 0.4210 target = 0.137229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.118786 restraints weight = 66350.982| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.87 r_work: 0.3807 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.7590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28498 Z= 0.175 Angle : 0.710 13.990 39044 Z= 0.362 Chirality : 0.043 0.297 4249 Planarity : 0.004 0.056 4666 Dihedral : 19.785 174.994 5142 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.83 % Favored : 89.78 % Rotamer: Outliers : 4.44 % Allowed : 27.01 % Favored : 68.55 % 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: -2.83 (0.14), residues: 3081 helix: -0.19 (0.15), residues: 1105 sheet: -2.87 (0.20), residues: 533 loop : -2.87 (0.14), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 146 HIS 0.008 0.001 HIS I 85 PHE 0.025 0.002 PHE I 101 TYR 0.032 0.002 TYR M 175 ARG 0.009 0.001 ARG N 90 Details of bonding type rmsd hydrogen bonds : bond 0.05671 ( 878) hydrogen bonds : angle 5.20639 ( 2455) covalent geometry : bond 0.00405 (28498) covalent geometry : angle 0.70978 (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 657 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 539 time to evaluate : 2.754 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 16 GLN cc_start: 0.7434 (mp10) cc_final: 0.6781 (mp10) REVERT: A 64 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.6224 (m-30) REVERT: A 116 MET cc_start: 0.5377 (mtp) cc_final: 0.4910 (ttt) REVERT: A 141 MET cc_start: 0.7710 (mpp) cc_final: 0.7357 (mpp) REVERT: A 150 MET cc_start: 0.7646 (ptp) cc_final: 0.7172 (ptp) REVERT: A 220 GLN cc_start: 0.8015 (tt0) cc_final: 0.7735 (tt0) REVERT: A 271 LYS cc_start: 0.8120 (pttt) cc_final: 0.7647 (ttmt) REVERT: B 33 ASP cc_start: 0.8145 (t0) cc_final: 0.7338 (t70) REVERT: B 64 ASP cc_start: 0.6137 (OUTLIER) cc_final: 0.5374 (m-30) REVERT: B 66 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3365 (m-80) REVERT: B 90 GLU cc_start: 0.7488 (tp30) cc_final: 0.6858 (tm-30) REVERT: B 204 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7173 (pp30) REVERT: B 211 ASP cc_start: 0.7475 (m-30) cc_final: 0.6977 (p0) REVERT: C 16 GLN cc_start: 0.6780 (mm-40) cc_final: 0.6320 (mm-40) REVERT: C 23 ASP cc_start: 0.7575 (t0) cc_final: 0.7255 (t0) REVERT: C 41 VAL cc_start: 0.8204 (t) cc_final: 0.7829 (t) REVERT: C 90 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7024 (tm-30) REVERT: C 107 TYR cc_start: 0.7520 (t80) cc_final: 0.7133 (t80) REVERT: C 134 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7721 (p) REVERT: C 150 MET cc_start: 0.8160 (ptm) cc_final: 0.7940 (ptp) REVERT: C 166 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7557 (p) REVERT: C 209 MET cc_start: 0.8241 (ptt) cc_final: 0.7890 (ttp) REVERT: D 23 ASP cc_start: 0.8237 (t0) cc_final: 0.7919 (t0) REVERT: D 66 PHE cc_start: 0.3878 (t80) cc_final: 0.2749 (t80) REVERT: D 67 ILE cc_start: 0.5542 (OUTLIER) cc_final: 0.5281 (mp) REVERT: D 106 TYR cc_start: 0.6945 (m-80) cc_final: 0.6358 (m-80) REVERT: D 141 MET cc_start: 0.8003 (mmt) cc_final: 0.7476 (mmt) REVERT: D 166 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6896 (p) REVERT: D 167 MET cc_start: 0.7757 (ttm) cc_final: 0.7152 (ttm) REVERT: D 220 GLN cc_start: 0.7762 (tt0) cc_final: 0.7406 (tt0) REVERT: D 221 MET cc_start: 0.8006 (mtm) cc_final: 0.7685 (mtp) REVERT: E 53 PHE cc_start: 0.6923 (t80) cc_final: 0.6683 (t80) REVERT: E 56 MET cc_start: 0.8152 (mmp) cc_final: 0.7941 (mmp) REVERT: E 66 PHE cc_start: 0.4174 (OUTLIER) cc_final: 0.3504 (m-80) REVERT: E 150 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5948 (mpp) REVERT: E 163 ASP cc_start: 0.3417 (OUTLIER) cc_final: 0.3166 (p0) REVERT: E 166 THR cc_start: 0.5107 (OUTLIER) cc_final: 0.4872 (p) REVERT: E 169 ARG cc_start: 0.7437 (mtp85) cc_final: 0.7152 (mmm160) REVERT: E 230 GLU cc_start: 0.6221 (mp0) cc_final: 0.5977 (mp0) REVERT: E 271 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5596 (mmtm) REVERT: F 53 PHE cc_start: 0.8064 (t80) cc_final: 0.7837 (t80) REVERT: F 93 GLU cc_start: 0.7808 (mp0) cc_final: 0.7591 (mp0) REVERT: F 116 MET cc_start: 0.7688 (mpp) cc_final: 0.7421 (mpp) REVERT: F 178 TYR cc_start: 0.6390 (m-80) cc_final: 0.5997 (m-80) REVERT: F 199 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7908 (pp) REVERT: F 204 GLN cc_start: 0.8866 (pt0) cc_final: 0.8583 (tm-30) REVERT: G 78 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7146 (tm-30) REVERT: G 83 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7355 (tt) REVERT: G 103 ILE cc_start: 0.7329 (mm) cc_final: 0.5949 (mm) REVERT: G 107 HIS cc_start: 0.7724 (m-70) cc_final: 0.6836 (m90) REVERT: H 1 MET cc_start: 0.7267 (ptt) cc_final: 0.6106 (tpp) REVERT: H 59 ARG cc_start: 0.7396 (mtp-110) cc_final: 0.6802 (mtp-110) REVERT: H 98 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: H 148 GLU cc_start: 0.7640 (tp30) cc_final: 0.7216 (tp30) REVERT: H 171 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: H 178 TYR cc_start: 0.8074 (t80) cc_final: 0.7648 (t80) REVERT: H 215 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8148 (m-40) REVERT: H 235 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6838 (tm-30) REVERT: H 271 THR cc_start: 0.9057 (m) cc_final: 0.8470 (p) REVERT: H 342 TRP cc_start: 0.8480 (t-100) cc_final: 0.7972 (t-100) REVERT: H 420 LEU cc_start: 0.9034 (mm) cc_final: 0.8763 (mp) REVERT: H 579 PHE cc_start: 0.8200 (t80) cc_final: 0.7813 (t80) REVERT: I 67 GLU cc_start: 0.9068 (pt0) cc_final: 0.8792 (pt0) REVERT: I 91 ASN cc_start: 0.8154 (m110) cc_final: 0.7860 (m-40) REVERT: J 65 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8667 (mmmt) REVERT: J 74 GLN cc_start: 0.8273 (mp10) cc_final: 0.7940 (mp10) REVERT: M 53 PHE cc_start: 0.8167 (t80) cc_final: 0.7592 (t80) REVERT: M 56 MET cc_start: 0.8511 (mtm) cc_final: 0.7992 (mtm) REVERT: M 63 HIS cc_start: 0.8255 (m-70) cc_final: 0.8037 (m-70) REVERT: M 66 PHE cc_start: 0.7658 (t80) cc_final: 0.6892 (t80) REVERT: M 116 MET cc_start: 0.8263 (mmp) cc_final: 0.7242 (tpt) REVERT: M 150 MET cc_start: 0.8520 (mtp) cc_final: 0.8032 (mtp) REVERT: M 167 MET cc_start: 0.8352 (tpp) cc_final: 0.8078 (tpp) REVERT: M 178 TYR cc_start: 0.9114 (m-80) cc_final: 0.7987 (m-80) REVERT: M 221 MET cc_start: 0.8724 (mtp) cc_final: 0.8318 (mmm) REVERT: N 25 SER cc_start: 0.8944 (p) cc_final: 0.8686 (m) REVERT: N 36 ASN cc_start: 0.6415 (m-40) cc_final: 0.6040 (m-40) REVERT: N 39 MET cc_start: 0.5928 (ptp) cc_final: 0.5723 (ptp) REVERT: N 64 ASN cc_start: 0.7622 (p0) cc_final: 0.7318 (p0) REVERT: N 69 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: N 123 GLU cc_start: 0.8987 (tp30) cc_final: 0.8293 (tm-30) REVERT: N 136 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.4916 (t-170) REVERT: N 140 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8330 (mm) REVERT: N 147 CYS cc_start: 0.6275 (m) cc_final: 0.5829 (m) REVERT: N 161 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.4860 (tt) REVERT: N 171 MET cc_start: 0.6349 (mtm) cc_final: 0.6089 (mtm) REVERT: N 175 MET cc_start: 0.7580 (mpp) cc_final: 0.7213 (mpp) REVERT: N 193 TYR cc_start: 0.8112 (t80) cc_final: 0.7422 (t80) outliers start: 118 outliers final: 66 residues processed: 615 average time/residue: 0.3803 time to fit residues: 369.2242 Evaluate side-chains 572 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 484 time to evaluate : 2.829 ------------------------------------------------------------------------------- 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 72 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 204 GLN 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 198 ASP Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 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 E residue 66 PHE Chi-restraints excluded: chain E residue 100 GLN 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 175 TYR 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 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 171 GLN 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 307 LEU 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 I residue 14 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 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 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 69 GLU Chi-restraints excluded: chain N residue 136 HIS 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 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: 1.9990 chunk 103 optimal weight: 1.9990 chunk 314 optimal weight: 0.1980 chunk 186 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 258 optimal weight: 0.0970 chunk 249 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 220 GLN D 191 GLN E 208 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN J 120 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.134169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.116311 restraints weight = 65754.813| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.71 r_work: 0.3768 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.7971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28498 Z= 0.194 Angle : 0.722 13.060 39044 Z= 0.370 Chirality : 0.043 0.247 4249 Planarity : 0.005 0.072 4666 Dihedral : 19.802 174.843 5142 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.42 % Favored : 89.16 % Rotamer: Outliers : 4.10 % Allowed : 27.95 % Favored : 67.95 % 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: -2.80 (0.14), residues: 3081 helix: -0.20 (0.15), residues: 1106 sheet: -2.85 (0.19), residues: 559 loop : -2.82 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 146 HIS 0.014 0.001 HIS N 136 PHE 0.032 0.002 PHE H 498 TYR 0.029 0.002 TYR M 175 ARG 0.012 0.001 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.05636 ( 878) hydrogen bonds : angle 5.23979 ( 2455) covalent geometry : bond 0.00445 (28498) covalent geometry : angle 0.72202 (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 634 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 525 time to evaluate : 2.836 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 4 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8492 (mp0) REVERT: A 16 GLN cc_start: 0.7476 (mp10) cc_final: 0.6834 (mp10) REVERT: A 64 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.6208 (m-30) REVERT: A 141 MET cc_start: 0.8138 (mpp) cc_final: 0.7713 (mpp) REVERT: A 150 MET cc_start: 0.7941 (ptp) cc_final: 0.7507 (ptp) REVERT: A 220 GLN cc_start: 0.7995 (tt0) cc_final: 0.7716 (tt0) REVERT: A 271 LYS cc_start: 0.8055 (pttt) cc_final: 0.7587 (ttmt) REVERT: B 33 ASP cc_start: 0.8336 (t0) cc_final: 0.7605 (t70) REVERT: B 64 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5380 (m-30) REVERT: B 66 PHE cc_start: 0.4423 (OUTLIER) cc_final: 0.3443 (m-80) REVERT: B 90 GLU cc_start: 0.7570 (tp30) cc_final: 0.6959 (tm-30) REVERT: B 141 MET cc_start: 0.7263 (mmt) cc_final: 0.6844 (mmm) REVERT: B 209 MET cc_start: 0.7638 (ptt) cc_final: 0.7242 (ptt) REVERT: B 211 ASP cc_start: 0.7619 (m-30) cc_final: 0.6897 (p0) REVERT: C 17 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6561 (t0) REVERT: C 23 ASP cc_start: 0.7617 (t0) cc_final: 0.7269 (t0) REVERT: C 41 VAL cc_start: 0.8355 (t) cc_final: 0.7956 (t) REVERT: C 103 CYS cc_start: 0.8426 (m) cc_final: 0.7494 (p) REVERT: C 116 MET cc_start: 0.8460 (mpp) cc_final: 0.8118 (mpp) REVERT: C 134 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7877 (p) REVERT: C 166 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7634 (p) REVERT: D 25 ASP cc_start: 0.7026 (t0) cc_final: 0.6321 (t0) REVERT: D 67 ILE cc_start: 0.5729 (OUTLIER) cc_final: 0.5383 (mp) REVERT: D 106 TYR cc_start: 0.7005 (m-80) cc_final: 0.6423 (m-80) REVERT: D 141 MET cc_start: 0.7982 (mmt) cc_final: 0.7443 (mmt) REVERT: D 166 THR cc_start: 0.7273 (OUTLIER) cc_final: 0.7011 (p) REVERT: D 214 HIS cc_start: 0.6955 (m170) cc_final: 0.6727 (m170) REVERT: D 220 GLN cc_start: 0.7824 (tt0) cc_final: 0.7474 (tt0) REVERT: D 221 MET cc_start: 0.8127 (mtm) cc_final: 0.7739 (mtp) REVERT: E 56 MET cc_start: 0.8180 (mmp) cc_final: 0.7954 (mmp) REVERT: E 66 PHE cc_start: 0.4186 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: E 106 TYR cc_start: 0.7334 (m-80) cc_final: 0.6263 (t80) REVERT: E 145 HIS cc_start: 0.8323 (m170) cc_final: 0.7958 (m170) REVERT: E 163 ASP cc_start: 0.3970 (OUTLIER) cc_final: 0.2366 (p0) REVERT: E 165 ARG cc_start: 0.7321 (mtt-85) cc_final: 0.7028 (mtt180) REVERT: E 166 THR cc_start: 0.4764 (OUTLIER) cc_final: 0.4554 (p) REVERT: E 169 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7316 (mmm160) REVERT: E 271 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.5881 (mmtm) REVERT: F 53 PHE cc_start: 0.8023 (t80) cc_final: 0.7704 (t80) REVERT: F 100 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8221 (mm110) REVERT: F 116 MET cc_start: 0.7657 (mpp) cc_final: 0.7455 (mpp) REVERT: F 141 MET cc_start: 0.0447 (ptp) cc_final: 0.0184 (ptt) REVERT: F 167 MET cc_start: 0.5835 (ptp) cc_final: 0.5433 (ptt) REVERT: F 178 TYR cc_start: 0.6429 (m-80) cc_final: 0.6125 (m-80) REVERT: F 199 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7904 (pp) REVERT: F 204 GLN cc_start: 0.8823 (pt0) cc_final: 0.8477 (tm-30) REVERT: F 220 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7270 (mm-40) REVERT: F 248 GLN cc_start: 0.6777 (mm-40) cc_final: 0.6519 (mm-40) REVERT: G 56 MET cc_start: 0.7733 (mmt) cc_final: 0.7481 (mmt) REVERT: G 78 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7148 (tm-30) REVERT: G 103 ILE cc_start: 0.7531 (mm) cc_final: 0.6261 (mm) REVERT: G 107 HIS cc_start: 0.7778 (m-70) cc_final: 0.6713 (m90) REVERT: H 1 MET cc_start: 0.7238 (ptt) cc_final: 0.6103 (tpt) REVERT: H 26 GLU cc_start: 0.8041 (pt0) cc_final: 0.7663 (pt0) REVERT: H 29 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8365 (tt0) REVERT: H 59 ARG cc_start: 0.7505 (mtp-110) cc_final: 0.6881 (mtp-110) REVERT: H 98 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: H 148 GLU cc_start: 0.7815 (tp30) cc_final: 0.7406 (tp30) REVERT: H 171 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: H 215 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8281 (m-40) REVERT: H 235 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6841 (tm-30) REVERT: H 271 THR cc_start: 0.9083 (m) cc_final: 0.8526 (p) REVERT: H 342 TRP cc_start: 0.8554 (t-100) cc_final: 0.8113 (t-100) REVERT: H 446 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7797 (ptp90) REVERT: H 579 PHE cc_start: 0.8194 (t80) cc_final: 0.7848 (t80) REVERT: I 65 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8572 (tppt) REVERT: I 67 GLU cc_start: 0.9052 (pt0) cc_final: 0.8668 (pt0) REVERT: I 68 PHE cc_start: 0.8388 (m-80) cc_final: 0.8136 (m-80) REVERT: I 75 LEU cc_start: 0.9193 (mt) cc_final: 0.8708 (mt) REVERT: I 91 ASN cc_start: 0.8261 (m110) cc_final: 0.7982 (m-40) REVERT: J 65 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8625 (mmmt) REVERT: J 74 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: J 84 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8715 (mm-30) REVERT: J 88 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8990 (ttt-90) REVERT: J 91 ASN cc_start: 0.8343 (m-40) cc_final: 0.7702 (m-40) REVERT: M 2 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7654 (m) REVERT: M 56 MET cc_start: 0.8502 (mtm) cc_final: 0.7925 (mtm) REVERT: M 63 HIS cc_start: 0.8297 (m-70) cc_final: 0.7992 (m-70) REVERT: M 66 PHE cc_start: 0.7848 (t80) cc_final: 0.7629 (t80) REVERT: M 108 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8197 (t70) REVERT: M 150 MET cc_start: 0.8518 (mtp) cc_final: 0.7871 (mtt) REVERT: M 167 MET cc_start: 0.8435 (tpp) cc_final: 0.8094 (tpp) REVERT: M 178 TYR cc_start: 0.9155 (m-80) cc_final: 0.7993 (m-80) REVERT: M 209 MET cc_start: 0.8890 (ptt) cc_final: 0.8479 (ttp) REVERT: N 25 SER cc_start: 0.9009 (p) cc_final: 0.8661 (m) REVERT: N 36 ASN cc_start: 0.6227 (m-40) cc_final: 0.5930 (m-40) REVERT: N 64 ASN cc_start: 0.7798 (p0) cc_final: 0.7550 (p0) REVERT: N 69 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: N 123 GLU cc_start: 0.8987 (tp30) cc_final: 0.8322 (tm-30) REVERT: N 136 HIS cc_start: 0.6457 (OUTLIER) cc_final: 0.5241 (t70) REVERT: N 147 CYS cc_start: 0.6180 (m) cc_final: 0.5646 (m) REVERT: N 161 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.4939 (tt) REVERT: N 175 MET cc_start: 0.7705 (mpp) cc_final: 0.7193 (mpp) REVERT: N 193 TYR cc_start: 0.8185 (t80) cc_final: 0.7890 (t80) outliers start: 109 outliers final: 64 residues processed: 603 average time/residue: 0.3854 time to fit residues: 368.8232 Evaluate side-chains 575 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 488 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 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 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 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 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 D residue 8 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 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 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 134 SER 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 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR 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 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 307 LEU 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 74 GLN Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 2 THR 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 220 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 542 HIS ** 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.131067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.112567 restraints weight = 66328.817| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.75 r_work: 0.3715 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.8411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28498 Z= 0.214 Angle : 0.756 16.223 39044 Z= 0.385 Chirality : 0.044 0.252 4249 Planarity : 0.005 0.064 4666 Dihedral : 19.801 174.081 5142 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.29 % Favored : 89.32 % Rotamer: Outliers : 4.06 % Allowed : 28.71 % Favored : 67.23 % 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: -2.80 (0.14), residues: 3081 helix: -0.29 (0.15), residues: 1119 sheet: -2.82 (0.19), residues: 559 loop : -2.77 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 146 HIS 0.009 0.001 HIS F 187 PHE 0.024 0.002 PHE N 125 TYR 0.027 0.002 TYR M 175 ARG 0.008 0.001 ARG C 48 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 878) hydrogen bonds : angle 5.28708 ( 2455) covalent geometry : bond 0.00491 (28498) covalent geometry : angle 0.75627 (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 621 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 513 time to evaluate : 2.788 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: 0.8724 (mm-30) cc_final: 0.8415 (mp0) REVERT: A 16 GLN cc_start: 0.7478 (mp10) cc_final: 0.6805 (mp10) REVERT: A 64 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: A 116 MET cc_start: 0.5968 (mtp) cc_final: 0.5727 (ttt) REVERT: A 141 MET cc_start: 0.7722 (mpp) cc_final: 0.7492 (mpp) REVERT: A 150 MET cc_start: 0.8079 (ptp) cc_final: 0.7588 (ptp) REVERT: A 220 GLN cc_start: 0.7984 (tt0) cc_final: 0.7721 (tt0) REVERT: A 245 LYS cc_start: 0.8552 (mttt) cc_final: 0.8348 (mmtt) REVERT: A 271 LYS cc_start: 0.8123 (pttt) cc_final: 0.7751 (ptmm) REVERT: B 33 ASP cc_start: 0.8615 (t0) cc_final: 0.8033 (t70) REVERT: B 66 PHE cc_start: 0.4743 (OUTLIER) cc_final: 0.3715 (m-80) REVERT: B 90 GLU cc_start: 0.7702 (tp30) cc_final: 0.7087 (tm-30) REVERT: B 141 MET cc_start: 0.7494 (mmt) cc_final: 0.7262 (tpp) REVERT: B 209 MET cc_start: 0.7844 (ptt) cc_final: 0.7418 (ptt) REVERT: B 211 ASP cc_start: 0.7856 (m-30) cc_final: 0.7068 (p0) REVERT: C 8 ASP cc_start: 0.8782 (m-30) cc_final: 0.8332 (m-30) REVERT: C 17 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6654 (t0) REVERT: C 23 ASP cc_start: 0.7635 (t0) cc_final: 0.7351 (t0) REVERT: C 93 GLU cc_start: 0.7776 (tp30) cc_final: 0.7480 (tp30) REVERT: C 103 CYS cc_start: 0.8556 (m) cc_final: 0.7763 (p) REVERT: C 116 MET cc_start: 0.8493 (mpp) cc_final: 0.8033 (mpp) REVERT: C 134 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8079 (p) REVERT: C 178 TYR cc_start: 0.8245 (m-10) cc_final: 0.7888 (m-10) REVERT: C 209 MET cc_start: 0.8440 (ptt) cc_final: 0.8003 (ttp) REVERT: C 252 LYS cc_start: 0.6556 (mttt) cc_final: 0.6355 (mttt) REVERT: D 23 ASP cc_start: 0.8012 (t0) cc_final: 0.7678 (t0) REVERT: D 25 ASP cc_start: 0.6873 (t0) cc_final: 0.6555 (t0) REVERT: D 67 ILE cc_start: 0.5680 (OUTLIER) cc_final: 0.5390 (mp) REVERT: D 90 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6722 (tm-30) REVERT: D 106 TYR cc_start: 0.7047 (m-80) cc_final: 0.6379 (m-80) REVERT: D 126 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7841 (tpt170) REVERT: D 141 MET cc_start: 0.8043 (mmt) cc_final: 0.7341 (mmt) REVERT: D 143 LEU cc_start: 0.8573 (mt) cc_final: 0.8142 (mt) REVERT: D 166 THR cc_start: 0.7092 (OUTLIER) cc_final: 0.6825 (p) REVERT: D 167 MET cc_start: 0.8284 (ttm) cc_final: 0.7907 (ttm) REVERT: D 214 HIS cc_start: 0.6992 (m170) cc_final: 0.6786 (m170) REVERT: D 220 GLN cc_start: 0.7858 (tt0) cc_final: 0.7567 (tt0) REVERT: D 221 MET cc_start: 0.8266 (mtm) cc_final: 0.7893 (mtp) REVERT: E 66 PHE cc_start: 0.4484 (OUTLIER) cc_final: 0.3925 (m-80) REVERT: E 143 LEU cc_start: 0.7978 (mt) cc_final: 0.6984 (mt) REVERT: E 145 HIS cc_start: 0.8073 (m170) cc_final: 0.7710 (m170) REVERT: E 163 ASP cc_start: 0.3737 (OUTLIER) cc_final: 0.2801 (p0) REVERT: E 165 ARG cc_start: 0.7439 (mtt-85) cc_final: 0.7095 (mtt180) REVERT: E 166 THR cc_start: 0.4954 (OUTLIER) cc_final: 0.4742 (p) REVERT: E 271 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6185 (mmtm) REVERT: F 53 PHE cc_start: 0.8038 (t80) cc_final: 0.7625 (t80) REVERT: F 100 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8327 (mm110) REVERT: F 116 MET cc_start: 0.8051 (mpp) cc_final: 0.7775 (mpp) REVERT: F 141 MET cc_start: 0.0374 (ptp) cc_final: 0.0120 (ptt) REVERT: F 167 MET cc_start: 0.5866 (ptp) cc_final: 0.5573 (ptp) REVERT: F 178 TYR cc_start: 0.6427 (m-80) cc_final: 0.6124 (m-80) REVERT: F 199 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7938 (pp) REVERT: F 204 GLN cc_start: 0.8805 (pt0) cc_final: 0.8594 (tm-30) REVERT: F 212 HIS cc_start: 0.5981 (p-80) cc_final: 0.5639 (p90) REVERT: F 220 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7283 (mm-40) REVERT: F 248 GLN cc_start: 0.6877 (mm-40) cc_final: 0.6663 (mm-40) REVERT: G 56 MET cc_start: 0.7912 (mmt) cc_final: 0.7687 (mmt) REVERT: G 74 GLN cc_start: 0.6106 (mp10) cc_final: 0.5854 (pm20) REVERT: G 103 ILE cc_start: 0.7570 (mm) cc_final: 0.6336 (mm) REVERT: G 107 HIS cc_start: 0.7777 (m-70) cc_final: 0.6730 (m90) REVERT: H 1 MET cc_start: 0.7154 (ptt) cc_final: 0.5889 (tpt) REVERT: H 26 GLU cc_start: 0.7974 (pt0) cc_final: 0.7631 (pt0) REVERT: H 59 ARG cc_start: 0.7446 (mtp-110) cc_final: 0.6999 (mtp-110) REVERT: H 98 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: H 148 GLU cc_start: 0.7771 (tp30) cc_final: 0.7353 (tp30) REVERT: H 171 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: H 215 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8322 (m-40) REVERT: H 235 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6576 (tm-30) REVERT: H 248 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7328 (t80) REVERT: H 271 THR cc_start: 0.9115 (m) cc_final: 0.8588 (p) REVERT: H 277 LYS cc_start: 0.8799 (tppp) cc_final: 0.8542 (tppt) REVERT: H 342 TRP cc_start: 0.8591 (t-100) cc_final: 0.8237 (t-100) REVERT: H 393 LEU cc_start: 0.8618 (mt) cc_final: 0.8375 (mp) REVERT: H 446 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7638 (ptp-170) REVERT: H 579 PHE cc_start: 0.8236 (t80) cc_final: 0.7912 (t80) REVERT: I 38 ASP cc_start: 0.8290 (m-30) cc_final: 0.7691 (m-30) REVERT: I 65 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8619 (tppt) REVERT: I 67 GLU cc_start: 0.9066 (pt0) cc_final: 0.8736 (pt0) REVERT: I 75 LEU cc_start: 0.9221 (mt) cc_final: 0.8621 (mt) REVERT: I 84 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8420 (tp30) REVERT: I 91 ASN cc_start: 0.8291 (m110) cc_final: 0.8040 (m-40) REVERT: J 65 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8722 (mmmt) REVERT: J 68 PHE cc_start: 0.8321 (m-80) cc_final: 0.7837 (m-80) REVERT: J 88 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8975 (ttt-90) REVERT: J 91 ASN cc_start: 0.8473 (m-40) cc_final: 0.7923 (m-40) REVERT: M 56 MET cc_start: 0.8536 (mtm) cc_final: 0.7953 (mtm) REVERT: M 116 MET cc_start: 0.8068 (mmp) cc_final: 0.7146 (tpt) REVERT: M 150 MET cc_start: 0.8566 (mtp) cc_final: 0.7922 (mtt) REVERT: M 167 MET cc_start: 0.8511 (tpp) cc_final: 0.8147 (tpp) REVERT: M 178 TYR cc_start: 0.9255 (m-80) cc_final: 0.8002 (m-80) REVERT: M 209 MET cc_start: 0.8937 (ptt) cc_final: 0.8529 (ttp) REVERT: M 221 MET cc_start: 0.8923 (mmm) cc_final: 0.8710 (mmm) REVERT: N 25 SER cc_start: 0.9032 (p) cc_final: 0.8711 (m) REVERT: N 36 ASN cc_start: 0.6417 (m-40) cc_final: 0.6069 (m-40) REVERT: N 64 ASN cc_start: 0.7872 (p0) cc_final: 0.7528 (p0) REVERT: N 69 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: N 123 GLU cc_start: 0.8901 (tp30) cc_final: 0.8292 (tm-30) REVERT: N 147 CYS cc_start: 0.6151 (m) cc_final: 0.5804 (m) REVERT: N 171 MET cc_start: 0.6656 (mtm) cc_final: 0.6407 (mtm) REVERT: N 175 MET cc_start: 0.7911 (mpp) cc_final: 0.7692 (mpp) REVERT: N 193 TYR cc_start: 0.8086 (t80) cc_final: 0.7852 (t80) outliers start: 108 outliers final: 69 residues processed: 587 average time/residue: 0.4084 time to fit residues: 379.6398 Evaluate side-chains 576 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 489 time to evaluate : 3.006 ------------------------------------------------------------------------------- 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 209 MET 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 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 68 ARG Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 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 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 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 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR 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 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 270 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 307 LEU 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 I residue 84 GLU 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 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 136 HIS Chi-restraints excluded: chain N residue 154 LYS 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: 0.9990 chunk 138 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 162 optimal weight: 0.0050 chunk 234 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN D 55 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 GLN ** 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** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.131107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.113269 restraints weight = 65618.385| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.67 r_work: 0.3713 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.8644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28498 Z= 0.189 Angle : 0.749 16.696 39044 Z= 0.381 Chirality : 0.044 0.241 4249 Planarity : 0.005 0.053 4666 Dihedral : 19.792 173.624 5142 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.83 % Favored : 89.74 % Rotamer: Outliers : 4.10 % Allowed : 28.93 % Favored : 66.97 % 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: -0.30 (0.15), residues: 1113 sheet: -2.74 (0.20), residues: 539 loop : -2.74 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP H 146 HIS 0.010 0.001 HIS H 518 PHE 0.026 0.002 PHE E 53 TYR 0.023 0.002 TYR B 7 ARG 0.011 0.001 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 878) hydrogen bonds : angle 5.31723 ( 2455) covalent geometry : bond 0.00438 (28498) covalent geometry : angle 0.74882 (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 638 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 529 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8423 (mp0) REVERT: A 16 GLN cc_start: 0.7341 (mp10) cc_final: 0.6699 (mp10) REVERT: A 64 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.5713 (m-30) REVERT: A 141 MET cc_start: 0.7670 (mpp) cc_final: 0.7430 (mpp) REVERT: A 150 MET cc_start: 0.7938 (ptp) cc_final: 0.7397 (ptp) REVERT: A 220 GLN cc_start: 0.7940 (tt0) cc_final: 0.7716 (tt0) REVERT: A 245 LYS cc_start: 0.8627 (mttt) cc_final: 0.8322 (mmtt) REVERT: A 271 LYS cc_start: 0.8108 (pttt) cc_final: 0.7753 (ptmm) REVERT: B 33 ASP cc_start: 0.8608 (t0) cc_final: 0.8015 (t70) REVERT: B 63 HIS cc_start: 0.8192 (m-70) cc_final: 0.7922 (m90) REVERT: B 66 PHE cc_start: 0.4643 (OUTLIER) cc_final: 0.3972 (m-80) REVERT: B 90 GLU cc_start: 0.7637 (tp30) cc_final: 0.6990 (tm-30) REVERT: B 96 GLU cc_start: 0.8065 (tp30) cc_final: 0.7575 (tm-30) REVERT: B 141 MET cc_start: 0.7400 (mmt) cc_final: 0.6818 (mmm) REVERT: B 169 ARG cc_start: 0.7470 (mtp85) cc_final: 0.7089 (mtp85) REVERT: B 209 MET cc_start: 0.7876 (ptt) cc_final: 0.7453 (ptt) REVERT: B 211 ASP cc_start: 0.7977 (m-30) cc_final: 0.7125 (p0) REVERT: C 8 ASP cc_start: 0.8676 (m-30) cc_final: 0.8316 (m-30) REVERT: C 23 ASP cc_start: 0.7530 (t0) cc_final: 0.7277 (t0) REVERT: C 41 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.7952 (t) REVERT: C 56 MET cc_start: 0.6230 (ptt) cc_final: 0.5790 (ptt) REVERT: C 93 GLU cc_start: 0.7835 (tp30) cc_final: 0.7519 (tp30) REVERT: C 134 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.7898 (p) REVERT: C 144 GLU cc_start: 0.8397 (tt0) cc_final: 0.8133 (tm-30) REVERT: C 167 MET cc_start: 0.7382 (mtp) cc_final: 0.7181 (mtp) REVERT: D 23 ASP cc_start: 0.7912 (t0) cc_final: 0.7600 (t0) REVERT: D 67 ILE cc_start: 0.5990 (OUTLIER) cc_final: 0.5696 (mp) REVERT: D 90 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6886 (tm-30) REVERT: D 106 TYR cc_start: 0.7046 (m-80) cc_final: 0.6395 (m-80) REVERT: D 141 MET cc_start: 0.7946 (mmt) cc_final: 0.7293 (mmt) REVERT: D 143 LEU cc_start: 0.8573 (mt) cc_final: 0.8068 (mt) REVERT: D 166 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6848 (p) REVERT: D 167 MET cc_start: 0.8313 (ttm) cc_final: 0.7883 (ttm) REVERT: D 214 HIS cc_start: 0.7003 (m170) cc_final: 0.6798 (m170) REVERT: D 220 GLN cc_start: 0.7734 (tt0) cc_final: 0.7464 (tt0) REVERT: D 221 MET cc_start: 0.8264 (mtm) cc_final: 0.7862 (mtp) REVERT: E 21 ASN cc_start: 0.8146 (t0) cc_final: 0.7549 (t0) REVERT: E 66 PHE cc_start: 0.4632 (OUTLIER) cc_final: 0.4093 (m-80) REVERT: E 145 HIS cc_start: 0.8126 (m170) cc_final: 0.7657 (m170) REVERT: E 163 ASP cc_start: 0.4212 (OUTLIER) cc_final: 0.3255 (p0) REVERT: E 165 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.7088 (mtt180) REVERT: E 211 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: F 53 PHE cc_start: 0.8135 (t80) cc_final: 0.7744 (t80) REVERT: F 100 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8346 (mm110) REVERT: F 116 MET cc_start: 0.8175 (mpp) cc_final: 0.7873 (mpp) REVERT: F 167 MET cc_start: 0.5872 (ptp) cc_final: 0.5589 (ptp) REVERT: F 178 TYR cc_start: 0.6570 (m-80) cc_final: 0.6280 (m-80) REVERT: F 199 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8098 (pp) REVERT: F 204 GLN cc_start: 0.8865 (pt0) cc_final: 0.8536 (tm-30) REVERT: F 212 HIS cc_start: 0.6241 (p-80) cc_final: 0.5959 (p90) REVERT: F 248 GLN cc_start: 0.6855 (mm-40) cc_final: 0.6498 (mm110) REVERT: G 56 MET cc_start: 0.7976 (mmt) cc_final: 0.7736 (mmt) REVERT: G 74 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.5894 (pm20) REVERT: G 103 ILE cc_start: 0.7467 (mm) cc_final: 0.6171 (mm) REVERT: G 107 HIS cc_start: 0.7708 (m-70) cc_final: 0.6566 (m90) REVERT: H 1 MET cc_start: 0.7144 (ptt) cc_final: 0.5889 (tpt) REVERT: H 26 GLU cc_start: 0.8001 (pt0) cc_final: 0.7638 (pt0) REVERT: H 59 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7160 (mtp-110) REVERT: H 98 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: H 148 GLU cc_start: 0.7740 (tp30) cc_final: 0.7344 (tp30) REVERT: H 171 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: H 215 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8439 (m-40) REVERT: H 235 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6619 (tm-30) REVERT: H 248 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7340 (t80) REVERT: H 271 THR cc_start: 0.9064 (m) cc_final: 0.8507 (p) REVERT: H 342 TRP cc_start: 0.8598 (t-100) cc_final: 0.8320 (t-100) REVERT: H 393 LEU cc_start: 0.8563 (mt) cc_final: 0.8287 (mp) REVERT: H 446 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7909 (ttp-110) REVERT: H 579 PHE cc_start: 0.8179 (t80) cc_final: 0.7846 (t80) REVERT: I 65 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8642 (tppt) REVERT: I 67 GLU cc_start: 0.9130 (pt0) cc_final: 0.8802 (pt0) REVERT: I 68 PHE cc_start: 0.8448 (m-80) cc_final: 0.8228 (m-80) REVERT: I 80 ARG cc_start: 0.8425 (mtm110) cc_final: 0.8203 (mtm110) REVERT: I 84 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: I 88 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7726 (tmt170) REVERT: I 91 ASN cc_start: 0.8197 (m110) cc_final: 0.7615 (m-40) REVERT: J 87 GLN cc_start: 0.8985 (tp40) cc_final: 0.8720 (tp40) REVERT: J 91 ASN cc_start: 0.8410 (m-40) cc_final: 0.7839 (m-40) REVERT: M 31 ARG cc_start: 0.7226 (ptp-170) cc_final: 0.7017 (ptp-170) REVERT: M 56 MET cc_start: 0.8553 (mtm) cc_final: 0.7947 (mtm) REVERT: M 116 MET cc_start: 0.8104 (mmp) cc_final: 0.7144 (tpt) REVERT: M 150 MET cc_start: 0.8351 (mtp) cc_final: 0.7723 (mtt) REVERT: M 167 MET cc_start: 0.8416 (tpp) cc_final: 0.8110 (tpp) REVERT: M 178 TYR cc_start: 0.9249 (m-80) cc_final: 0.7962 (m-80) REVERT: M 209 MET cc_start: 0.8918 (ptt) cc_final: 0.8527 (ttp) REVERT: N 36 ASN cc_start: 0.6163 (m-40) cc_final: 0.5820 (m-40) REVERT: N 69 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: N 123 GLU cc_start: 0.8872 (tp30) cc_final: 0.8296 (tm-30) REVERT: N 136 HIS cc_start: 0.5799 (OUTLIER) cc_final: 0.4314 (t70) REVERT: N 147 CYS cc_start: 0.6457 (m) cc_final: 0.6114 (m) REVERT: N 161 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.4487 (tt) REVERT: N 175 MET cc_start: 0.8011 (mpp) cc_final: 0.7808 (mpp) REVERT: N 193 TYR cc_start: 0.8048 (t80) cc_final: 0.7787 (t80) outliers start: 109 outliers final: 70 residues processed: 595 average time/residue: 0.4060 time to fit residues: 377.5204 Evaluate side-chains 588 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 498 time to evaluate : 2.883 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain B residue 66 PHE 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 15 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 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 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 211 ASP Chi-restraints excluded: chain F residue 15 VAL 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 74 GLN 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 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 307 LEU 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 H residue 518 HIS Chi-restraints excluded: chain I residue 14 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 54 THR Chi-restraints excluded: chain J residue 74 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 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 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 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: 2.9990 chunk 159 optimal weight: 0.9990 chunk 238 optimal weight: 0.5980 chunk 242 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 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** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 GLN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 490 ASN I 74 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.129251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.111625 restraints weight = 65862.065| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.57 r_work: 0.3701 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.8919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28498 Z= 0.194 Angle : 0.753 16.100 39044 Z= 0.383 Chirality : 0.044 0.228 4249 Planarity : 0.005 0.055 4666 Dihedral : 19.792 173.776 5142 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.16 % Favored : 89.42 % Rotamer: Outliers : 3.88 % Allowed : 29.46 % Favored : 66.67 % 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: -2.76 (0.14), residues: 3081 helix: -0.31 (0.15), residues: 1108 sheet: -2.72 (0.20), residues: 539 loop : -2.71 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP H 146 HIS 0.012 0.001 HIS B 145 PHE 0.030 0.002 PHE C 261 TYR 0.024 0.002 TYR B 7 ARG 0.009 0.001 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 878) hydrogen bonds : angle 5.32644 ( 2455) covalent geometry : bond 0.00449 (28498) covalent geometry : angle 0.75258 (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 619 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 516 time to evaluate : 3.118 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: A 4 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8402 (mp0) REVERT: A 16 GLN cc_start: 0.7368 (mp10) cc_final: 0.6754 (mp10) REVERT: A 64 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.5752 (m-30) REVERT: A 141 MET cc_start: 0.7680 (mpp) cc_final: 0.7431 (mpp) REVERT: A 150 MET cc_start: 0.7929 (ptp) cc_final: 0.7438 (ptp) REVERT: A 220 GLN cc_start: 0.7929 (tt0) cc_final: 0.7703 (tt0) REVERT: A 245 LYS cc_start: 0.8624 (mttt) cc_final: 0.8284 (mmtt) REVERT: A 271 LYS cc_start: 0.8245 (pttt) cc_final: 0.7805 (ptmm) REVERT: B 33 ASP cc_start: 0.8635 (t0) cc_final: 0.8065 (t70) REVERT: B 66 PHE cc_start: 0.4683 (OUTLIER) cc_final: 0.3956 (m-10) REVERT: B 90 GLU cc_start: 0.7705 (tp30) cc_final: 0.7050 (tm-30) REVERT: B 96 GLU cc_start: 0.8123 (tp30) cc_final: 0.7650 (tm-30) REVERT: B 141 MET cc_start: 0.7458 (mmt) cc_final: 0.6839 (tpp) REVERT: B 209 MET cc_start: 0.7977 (ptt) cc_final: 0.7588 (ptt) REVERT: C 23 ASP cc_start: 0.7534 (t0) cc_final: 0.7332 (t0) REVERT: C 41 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8059 (t) REVERT: C 56 MET cc_start: 0.6490 (ptt) cc_final: 0.6062 (ptt) REVERT: C 93 GLU cc_start: 0.7956 (tp30) cc_final: 0.7630 (tp30) REVERT: C 103 CYS cc_start: 0.8348 (m) cc_final: 0.7689 (p) REVERT: C 134 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.7977 (p) REVERT: C 144 GLU cc_start: 0.8462 (tt0) cc_final: 0.8104 (tm-30) REVERT: D 25 ASP cc_start: 0.7331 (t0) cc_final: 0.7108 (t0) REVERT: D 67 ILE cc_start: 0.5952 (OUTLIER) cc_final: 0.5635 (mp) REVERT: D 68 ARG cc_start: 0.7699 (mmm-85) cc_final: 0.7493 (mmm-85) REVERT: D 90 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6910 (tm-30) REVERT: D 106 TYR cc_start: 0.7086 (m-80) cc_final: 0.6317 (m-80) REVERT: D 141 MET cc_start: 0.7968 (mmt) cc_final: 0.7271 (mmt) REVERT: D 143 LEU cc_start: 0.8575 (mt) cc_final: 0.8024 (mt) REVERT: D 156 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6325 (mmmt) REVERT: D 166 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6865 (p) REVERT: D 167 MET cc_start: 0.8329 (ttm) cc_final: 0.7885 (ttm) REVERT: D 220 GLN cc_start: 0.7773 (tt0) cc_final: 0.7538 (tt0) REVERT: D 221 MET cc_start: 0.8318 (mtm) cc_final: 0.7939 (mtp) REVERT: E 21 ASN cc_start: 0.7967 (t0) cc_final: 0.7535 (t0) REVERT: E 66 PHE cc_start: 0.4645 (OUTLIER) cc_final: 0.4118 (m-80) REVERT: E 102 MET cc_start: 0.8520 (ttm) cc_final: 0.8242 (tmm) REVERT: E 145 HIS cc_start: 0.8317 (m170) cc_final: 0.7765 (m170) REVERT: E 163 ASP cc_start: 0.4219 (OUTLIER) cc_final: 0.3365 (p0) REVERT: E 171 PHE cc_start: 0.8072 (m-80) cc_final: 0.7582 (m-80) REVERT: E 220 GLN cc_start: 0.8022 (tt0) cc_final: 0.7713 (tm-30) REVERT: E 221 MET cc_start: 0.8587 (mmt) cc_final: 0.7362 (mmt) REVERT: F 53 PHE cc_start: 0.8099 (t80) cc_final: 0.7620 (t80) REVERT: F 100 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8223 (mm110) REVERT: F 116 MET cc_start: 0.8165 (mpp) cc_final: 0.7845 (mpp) REVERT: F 167 MET cc_start: 0.5853 (ptp) cc_final: 0.5413 (ptt) REVERT: F 178 TYR cc_start: 0.6549 (m-80) cc_final: 0.6272 (m-80) REVERT: F 199 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7943 (pp) REVERT: F 204 GLN cc_start: 0.8930 (pt0) cc_final: 0.8618 (tm-30) REVERT: F 212 HIS cc_start: 0.6152 (p-80) cc_final: 0.5795 (p90) REVERT: F 248 GLN cc_start: 0.6866 (mm-40) cc_final: 0.6537 (mm110) REVERT: G 68 PHE cc_start: 0.5712 (m-80) cc_final: 0.5116 (m-80) REVERT: G 78 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7535 (tm-30) REVERT: G 103 ILE cc_start: 0.7540 (mm) cc_final: 0.6216 (mm) REVERT: G 107 HIS cc_start: 0.7724 (m-70) cc_final: 0.6535 (m90) REVERT: H 1 MET cc_start: 0.7114 (ptt) cc_final: 0.5830 (tpt) REVERT: H 26 GLU cc_start: 0.7971 (pt0) cc_final: 0.7592 (pt0) REVERT: H 59 ARG cc_start: 0.7642 (mtp-110) cc_final: 0.7167 (mtp-110) REVERT: H 98 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: H 148 GLU cc_start: 0.7745 (tp30) cc_final: 0.7353 (tp30) REVERT: H 171 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: H 215 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8393 (m-40) REVERT: H 235 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6638 (tm-30) REVERT: H 248 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7270 (t80) REVERT: H 271 THR cc_start: 0.9071 (m) cc_final: 0.8751 (p) REVERT: H 342 TRP cc_start: 0.8548 (t-100) cc_final: 0.8248 (t-100) REVERT: H 446 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7889 (ptp90) REVERT: H 579 PHE cc_start: 0.8239 (t80) cc_final: 0.7943 (t80) REVERT: I 65 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8639 (tppt) REVERT: I 68 PHE cc_start: 0.8437 (m-80) cc_final: 0.8017 (m-80) REVERT: I 80 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8258 (mtm110) REVERT: I 84 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: I 87 GLN cc_start: 0.8349 (tp-100) cc_final: 0.7835 (tp-100) REVERT: I 88 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7769 (tmt170) REVERT: I 91 ASN cc_start: 0.8217 (m110) cc_final: 0.7634 (m-40) REVERT: J 65 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8493 (mmmt) REVERT: J 87 GLN cc_start: 0.8976 (tp40) cc_final: 0.8721 (tp40) REVERT: J 91 ASN cc_start: 0.8381 (m-40) cc_final: 0.7827 (m-40) REVERT: M 53 PHE cc_start: 0.8195 (t80) cc_final: 0.7512 (t80) REVERT: M 56 MET cc_start: 0.8566 (mtm) cc_final: 0.8242 (mtm) REVERT: M 63 HIS cc_start: 0.8349 (m-70) cc_final: 0.8130 (m-70) REVERT: M 116 MET cc_start: 0.8134 (mmp) cc_final: 0.7187 (tpt) REVERT: M 150 MET cc_start: 0.8259 (mtp) cc_final: 0.7654 (mtt) REVERT: M 167 MET cc_start: 0.8392 (tpp) cc_final: 0.8093 (tpp) REVERT: M 178 TYR cc_start: 0.9266 (m-80) cc_final: 0.7996 (m-80) REVERT: M 209 MET cc_start: 0.8921 (ptt) cc_final: 0.8490 (ttp) REVERT: M 221 MET cc_start: 0.8829 (mmm) cc_final: 0.8319 (tpp) REVERT: N 36 ASN cc_start: 0.6232 (m-40) cc_final: 0.5879 (m-40) REVERT: N 65 ILE cc_start: 0.7063 (pt) cc_final: 0.6849 (pt) REVERT: N 69 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: N 123 GLU cc_start: 0.8744 (tp30) cc_final: 0.8276 (tm-30) REVERT: N 136 HIS cc_start: 0.6050 (OUTLIER) cc_final: 0.4520 (t70) REVERT: N 147 CYS cc_start: 0.6344 (m) cc_final: 0.6052 (m) REVERT: N 161 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.4326 (tt) REVERT: N 175 MET cc_start: 0.8089 (mpp) cc_final: 0.7506 (mpp) REVERT: N 193 TYR cc_start: 0.8112 (t80) cc_final: 0.7855 (t80) outliers start: 103 outliers final: 70 residues processed: 583 average time/residue: 0.4023 time to fit residues: 366.4707 Evaluate side-chains 583 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 494 time to evaluate : 3.035 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 PHE 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 15 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 12 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 206 LEU Chi-restraints excluded: chain F residue 15 VAL 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 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 307 LEU Chi-restraints excluded: chain H residue 402 THR 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 79 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 74 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 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 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 90 ARG Chi-restraints excluded: chain N residue 131 LYS 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: 2.9990 chunk 223 optimal weight: 2.9990 chunk 272 optimal weight: 0.0030 chunk 241 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 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** ** C 19 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 214 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 220 GLN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.129098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.111212 restraints weight = 65956.759| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.61 r_work: 0.3693 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.9080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28498 Z= 0.187 Angle : 0.769 16.047 39044 Z= 0.386 Chirality : 0.044 0.202 4249 Planarity : 0.005 0.058 4666 Dihedral : 19.782 173.389 5142 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.45 % Favored : 89.16 % Rotamer: Outliers : 3.61 % Allowed : 29.98 % Favored : 66.40 % 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: -2.82 (0.14), residues: 3081 helix: -0.37 (0.15), residues: 1112 sheet: -2.71 (0.20), residues: 539 loop : -2.76 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP H 146 HIS 0.012 0.001 HIS D 214 PHE 0.028 0.002 PHE M 66 TYR 0.024 0.002 TYR G 106 ARG 0.009 0.001 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.05708 ( 878) hydrogen bonds : angle 5.31839 ( 2455) covalent geometry : bond 0.00436 (28498) covalent geometry : angle 0.76863 (39044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13379.44 seconds wall clock time: 233 minutes 10.18 seconds (13990.18 seconds total)