Starting phenix.real_space_refine on Sat Aug 8 09:14:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gan_29901/08_2026/8gan_29901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gan_29901/08_2026/8gan_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2026/8gan_29901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2026/8gan_29901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2026/8gan_29901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2026/8gan_29901.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 5.98, per 1000 atoms: 0.22 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 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: 3.28 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: 5.29 Time building geometry restraints manager: 3.22 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=" C3' DT Q 12 " pdb=" C2' DT Q 12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C1' DT L 46 " pdb=" N1 DT L 46 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" C3' DG L 9 " pdb=" C2' DG L 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA O 18 " pdb=" C2' DA O 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA Q 8 " pdb=" C2' DA Q 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.87e+00 ... (remaining 28493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 38089 1.51 - 3.03: 854 3.03 - 4.54: 77 4.54 - 6.06: 22 6.06 - 7.57: 2 Bond angle restraints: 39044 Sorted by residual: angle pdb=" C1' C K 38 " pdb=" N1 C K 38 " pdb=" C2 C K 38 " ideal model delta sigma weight residual 118.80 126.37 -7.57 1.10e+00 8.26e-01 4.74e+01 angle pdb=" N1 C K 38 " pdb=" C2 C K 38 " pdb=" O2 C K 38 " ideal model delta sigma weight residual 118.90 122.63 -3.73 6.00e-01 2.78e+00 3.86e+01 angle pdb=" O4' DG L 38 " pdb=" C4' DG L 38 " pdb=" C3' DG L 38 " ideal model delta sigma weight residual 106.00 102.66 3.34 6.00e-01 2.78e+00 3.09e+01 angle pdb=" C3' G K 4 " pdb=" O3' G K 4 " pdb=" P A K 5 " ideal model delta sigma weight residual 119.70 125.66 -5.96 1.20e+00 6.94e-01 2.47e+01 angle pdb=" O2 C K 38 " pdb=" C2 C K 38 " pdb=" N3 C K 38 " ideal model delta sigma weight residual 121.90 118.47 3.43 7.00e-01 2.04e+00 2.40e+01 ... (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: 3520 0.050 - 0.100: 627 0.100 - 0.151: 92 0.151 - 0.201: 7 0.201 - 0.251: 3 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=" C3' G K 4 " pdb=" C4' G K 4 " pdb=" O3' G K 4 " pdb=" C2' G K 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4246 not shown) Planarity restraints: 4666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A K 6 " 0.031 2.00e-02 2.50e+03 1.38e-02 5.20e+00 pdb=" N9 A K 6 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A K 6 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A K 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A K 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A K 6 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A K 6 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A K 6 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A K 6 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C K 31 " 0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 C K 31 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C K 31 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C K 31 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C K 31 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C K 31 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C K 31 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C K 31 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C K 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 514 " -0.164 9.50e-02 1.11e+02 7.36e-02 3.43e+00 pdb=" NE ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 514 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 514 " -0.008 2.00e-02 2.50e+03 ... (remaining 4663 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 516 2.63 - 3.20: 23692 3.20 - 3.76: 47482 3.76 - 4.33: 65574 4.33 - 4.90: 104393 Nonbonded interactions: 241657 Sorted by model distance: nonbonded pdb=" N2 G K 30 " pdb=" O2 DC L 25 " model vdw 2.060 2.496 nonbonded pdb=" O THR A 148 " pdb=" O2' C K 31 " model vdw 2.135 3.040 nonbonded pdb=" O THR B 148 " pdb=" O2' U K 19 " model vdw 2.144 3.040 nonbonded pdb=" N2 G K 27 " pdb=" O2 DC L 28 " model vdw 2.161 2.496 nonbonded pdb=" O2 C K 43 " pdb=" N2 DG L 12 " model vdw 2.179 2.496 ... (remaining 241652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.310 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28498 Z= 0.220 Angle : 0.499 7.574 39044 Z= 0.375 Chirality : 0.039 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG H 514 TYR 0.013 0.001 TYR H 250 PHE 0.008 0.001 PHE N 192 TRP 0.005 0.001 TRP M 203 HIS 0.001 0.000 HIS G 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.22 (28498) covalent geometry : angle 0.49935 / 0.38 (39044) hydrogen bonds : bond 0.18318 / 11.64 ( 878) hydrogen bonds : angle 6.41266 / 4.54 ( 2455) *********************** 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 : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.2211 (OUTLIER) cc_final: 0.2000 (m-80) REVERT: B 150 MET cc_start: 0.5834 (ptm) cc_final: 0.5578 (ptm) REVERT: C 66 PHE cc_start: 0.2217 (OUTLIER) cc_final: 0.1565 (m-80) REVERT: C 150 MET cc_start: 0.5846 (ptm) cc_final: 0.5394 (ptm) REVERT: D 53 PHE cc_start: 0.1101 (t80) cc_final: 0.0790 (t80) REVERT: D 153 THR cc_start: 0.3888 (OUTLIER) cc_final: 0.3650 (m) REVERT: E 273 LEU cc_start: 0.3861 (pp) cc_final: 0.3344 (tp) REVERT: F 66 PHE cc_start: 0.3434 (OUTLIER) cc_final: 0.1845 (t80) REVERT: F 214 HIS cc_start: 0.4919 (m-70) cc_final: 0.4656 (m-70) REVERT: G 21 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7730 (mt) REVERT: H 48 THR cc_start: 0.6527 (p) cc_final: 0.6286 (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: 0.7454 (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: 0.6071 (Cg_endo) REVERT: H 549 HIS cc_start: 0.6907 (t-90) cc_final: 0.6589 (t-90) REVERT: M 148 THR cc_start: 0.7427 (m) cc_final: 0.7164 (m) REVERT: N 36 ASN cc_start: 0.2953 (m-40) cc_final: 0.2551 (m-40) REVERT: N 83 ILE cc_start: 0.6968 (pt) cc_final: 0.6506 (pt) outliers start: 81 outliers final: 10 residues processed: 1072 average time/residue: 0.1915 time to fit residues: 315.9921 Evaluate side-chains 594 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 579 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.4980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS A 234 ASN ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 145 HIS B 181 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 197 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 234 ASN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 145 HIS D 181 HIS D 191 GLN D 204 GLN D 231 HIS E 21 ASN E 55 GLN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 124 GLN E 181 HIS ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN F 55 GLN F 83 GLN F 231 HIS ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 HIS ** H 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 ASN ** H 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN H 538 GLN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 ASN N 61 GLN N 68 ASN N 88 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.168640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.152622 restraints weight = 68969.460| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 4.14 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28498 Z= 0.213 Angle : 0.828 13.675 39044 Z= 0.433 Chirality : 0.049 0.395 4249 Planarity : 0.006 0.059 4666 Dihedral : 19.659 175.582 5160 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.20 % Favored : 88.32 % Rotamer: Outliers : 4.59 % Allowed : 24.49 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.14), residues: 3081 helix: -0.44 (0.15), residues: 1101 sheet: -3.25 (0.22), residues: 445 loop : -3.34 (0.13), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 143 TYR 0.028 0.003 TYR H 312 PHE 0.023 0.003 PHE D 171 TRP 0.030 0.003 TRP J 77 HIS 0.012 0.002 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (28498) covalent geometry : angle 0.82798 / 0.43 (39044) hydrogen bonds : bond 0.06772 / 4.12 ( 878) hydrogen bonds : angle 5.49490 / 3.83 ( 2455) *********************** 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 753 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 631 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7652 (tmm) cc_final: 0.7440 (tmm) REVERT: B 100 GLN cc_start: 0.7307 (tp40) cc_final: 0.7079 (tp40) REVERT: B 109 ILE cc_start: 0.8151 (mt) cc_final: 0.7769 (mt) REVERT: B 165 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.6987 (mtt-85) REVERT: B 230 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6453 (tp30) REVERT: B 273 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7007 (pp) REVERT: C 23 ASP cc_start: 0.7498 (t0) cc_final: 0.6942 (t0) REVERT: C 40 LEU cc_start: 0.3634 (mt) cc_final: 0.3368 (mt) REVERT: C 41 VAL cc_start: 0.6534 (OUTLIER) cc_final: 0.6135 (t) REVERT: C 66 PHE cc_start: 0.1169 (OUTLIER) cc_final: 0.0846 (m-80) REVERT: D 25 ASP cc_start: 0.6825 (OUTLIER) cc_final: 0.6428 (t0) REVERT: D 62 HIS cc_start: 0.8196 (t-90) cc_final: 0.7732 (t70) REVERT: D 93 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7783 (mm-30) REVERT: D 107 TYR cc_start: 0.6140 (t80) cc_final: 0.5932 (t80) REVERT: D 167 MET cc_start: 0.6714 (ttm) cc_final: 0.6318 (ttm) REVERT: E 4 GLU cc_start: 0.7508 (pm20) cc_final: 0.7138 (pm20) REVERT: E 11 PHE cc_start: 0.4461 (t80) cc_final: 0.4259 (t80) REVERT: E 93 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7311 (tm-30) REVERT: E 171 PHE cc_start: 0.7092 (m-80) cc_final: 0.6522 (m-80) REVERT: E 204 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8184 (pp30) REVERT: E 272 ASN cc_start: 0.7028 (OUTLIER) cc_final: 0.6765 (t0) REVERT: F 56 MET cc_start: 0.6583 (ptp) cc_final: 0.6079 (ptp) REVERT: F 66 PHE cc_start: 0.3230 (OUTLIER) cc_final: 0.1985 (t80) REVERT: F 96 GLU cc_start: 0.7353 (tp30) cc_final: 0.7113 (tp30) REVERT: F 109 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8402 (mm) REVERT: H 29 GLU cc_start: 0.8324 (tt0) cc_final: 0.7472 (tp30) REVERT: H 149 CYS cc_start: 0.5936 (OUTLIER) cc_final: 0.4875 (p) REVERT: H 249 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6833 (mp0) REVERT: H 420 LEU cc_start: 0.8813 (mp) cc_final: 0.8560 (mp) REVERT: I 40 TYR cc_start: 0.7657 (m-10) cc_final: 0.7317 (m-10) REVERT: I 91 ASN cc_start: 0.7018 (m-40) cc_final: 0.6602 (m-40) REVERT: I 98 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7396 (tp40) REVERT: J 65 LYS cc_start: 0.8161 (tttp) cc_final: 0.7949 (ttpt) REVERT: M 64 ASP cc_start: 0.8138 (m-30) cc_final: 0.7726 (m-30) REVERT: M 178 TYR cc_start: 0.8447 (m-80) cc_final: 0.8058 (m-80) REVERT: M 269 ASP cc_start: 0.7118 (t0) cc_final: 0.6912 (t0) REVERT: N 36 ASN cc_start: 0.4984 (m-40) cc_final: 0.4645 (m-40) REVERT: N 50 LYS cc_start: 0.6898 (pttm) cc_final: 0.6590 (pttm) REVERT: N 161 LEU cc_start: 0.4759 (OUTLIER) cc_final: 0.3888 (tt) outliers start: 122 outliers final: 49 residues processed: 701 average time/residue: 0.1782 time to fit residues: 198.0625 Evaluate side-chains 570 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 509 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 103 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 272 ASN 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 109 ILE Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 38 ASP 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 215 SER Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR 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 306 optimal weight: 0.6980 chunk 314 optimal weight: 0.1980 chunk 198 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 307 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 58 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS A 234 ASN ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 19 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 220 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN E 208 ASN ** E 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS H 313 ASN ** H 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 HIS ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 231 HIS ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 HIS ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.166746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.149813 restraints weight = 70704.365| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 4.21 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28498 Z= 0.179 Angle : 0.755 17.821 39044 Z= 0.391 Chirality : 0.046 0.393 4249 Planarity : 0.005 0.057 4666 Dihedral : 19.644 176.144 5149 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.72 % Favored : 87.86 % Rotamer: Outliers : 4.51 % Allowed : 24.12 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.14), residues: 3081 helix: -0.45 (0.15), residues: 1114 sheet: -2.91 (0.22), residues: 460 loop : -3.35 (0.13), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 224 TYR 0.036 0.002 TYR N 26 PHE 0.024 0.002 PHE F 53 TRP 0.038 0.002 TRP J 77 HIS 0.015 0.002 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (28498) covalent geometry : angle 0.75497 / 0.39 (39044) hydrogen bonds : bond 0.06474 / 3.99 ( 878) hydrogen bonds : angle 5.43099 / 3.83 ( 2455) *********************** 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 688 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 568 time to evaluate : 1.033 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: A 16 GLN cc_start: 0.7104 (mp10) cc_final: 0.6434 (tm-30) REVERT: A 21 ASN cc_start: 0.7135 (t0) cc_final: 0.6697 (t0) REVERT: A 40 LEU cc_start: 0.5875 (tt) cc_final: 0.5126 (mt) REVERT: A 56 MET cc_start: 0.4592 (mtp) cc_final: 0.4021 (mtt) REVERT: A 150 MET cc_start: 0.5255 (ptp) cc_final: 0.4952 (ptp) REVERT: B 109 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7748 (mt) REVERT: B 264 TYR cc_start: 0.4622 (OUTLIER) cc_final: 0.3348 (m-80) REVERT: B 273 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7222 (pp) REVERT: C 23 ASP cc_start: 0.7193 (t0) cc_final: 0.6885 (t70) REVERT: C 25 ASP cc_start: 0.7133 (m-30) cc_final: 0.6240 (m-30) REVERT: C 64 ASP cc_start: 0.4607 (OUTLIER) cc_final: 0.4027 (m-30) REVERT: C 66 PHE cc_start: 0.1241 (OUTLIER) cc_final: 0.1020 (m-80) REVERT: C 79 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: C 150 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6587 (ptm) REVERT: C 157 ASP cc_start: 0.7336 (m-30) cc_final: 0.7037 (m-30) REVERT: C 169 ARG cc_start: 0.7378 (mtp85) cc_final: 0.6923 (mtp85) REVERT: C 271 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8281 (mmtt) REVERT: D 25 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6506 (t0) REVERT: D 93 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7607 (mm-30) REVERT: D 166 THR cc_start: 0.5764 (OUTLIER) cc_final: 0.5493 (p) REVERT: D 167 MET cc_start: 0.7080 (ttm) cc_final: 0.6693 (ttm) REVERT: E 40 LEU cc_start: 0.4755 (tt) cc_final: 0.3490 (mt) REVERT: E 204 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8095 (pp30) REVERT: E 206 LEU cc_start: 0.8147 (tp) cc_final: 0.7661 (tp) REVERT: F 66 PHE cc_start: 0.3205 (OUTLIER) cc_final: 0.1877 (t80) REVERT: G 21 LEU cc_start: 0.8504 (mt) cc_final: 0.8261 (mt) REVERT: G 77 TRP cc_start: 0.6452 (t60) cc_final: 0.6112 (t60) REVERT: H 29 GLU cc_start: 0.8244 (tt0) cc_final: 0.7455 (tp30) REVERT: H 146 TRP cc_start: 0.7742 (t60) cc_final: 0.7246 (t60) REVERT: H 215 ASN cc_start: 0.8243 (m110) cc_final: 0.7756 (m-40) REVERT: H 249 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6794 (mp0) REVERT: H 420 LEU cc_start: 0.8782 (mp) cc_final: 0.8424 (mp) REVERT: H 563 TYR cc_start: 0.8181 (t80) cc_final: 0.7960 (t80) REVERT: I 40 TYR cc_start: 0.7819 (m-10) cc_final: 0.7553 (m-10) REVERT: I 56 MET cc_start: 0.8870 (mmm) cc_final: 0.8433 (mmt) REVERT: I 91 ASN cc_start: 0.7220 (m-40) cc_final: 0.6863 (m-40) REVERT: I 96 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7521 (mt-10) REVERT: I 98 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7912 (tp-100) REVERT: I 119 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7935 (mtmm) REVERT: J 65 LYS cc_start: 0.8207 (tttp) cc_final: 0.7909 (ttpt) REVERT: J 77 TRP cc_start: 0.7303 (t60) cc_final: 0.6821 (t60) REVERT: M 47 LYS cc_start: 0.8024 (mptt) cc_final: 0.7648 (mppt) REVERT: M 64 ASP cc_start: 0.8133 (m-30) cc_final: 0.7638 (m-30) REVERT: M 116 MET cc_start: 0.7637 (mmt) cc_final: 0.7263 (tpp) REVERT: M 178 TYR cc_start: 0.8474 (m-80) cc_final: 0.8102 (m-80) REVERT: N 65 ILE cc_start: 0.7351 (tp) cc_final: 0.7149 (pt) REVERT: N 81 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7401 (tt) REVERT: N 123 GLU cc_start: 0.8269 (tp30) cc_final: 0.7820 (tm-30) REVERT: N 124 MET cc_start: 0.7807 (ptp) cc_final: 0.7250 (ptp) REVERT: N 161 LEU cc_start: 0.4745 (OUTLIER) cc_final: 0.3735 (tt) REVERT: N 193 TYR cc_start: 0.7678 (t80) cc_final: 0.7363 (t80) outliers start: 120 outliers final: 59 residues processed: 627 average time/residue: 0.1764 time to fit residues: 179.8785 Evaluate side-chains 568 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 494 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 111 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 109 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 153 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 66 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 29 ILE 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 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 291 optimal weight: 0.0050 chunk 129 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 115 optimal weight: 0.0770 chunk 196 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 overall best weight: 0.7756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 145 HIS ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN E 208 ASN F 204 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS G 98 GLN H 313 ASN ** H 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 GLN ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 HIS M 121 ASN N 68 ASN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.160740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.143004 restraints weight = 68906.363| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 4.10 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4722 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= 0.183 Angle : 0.742 16.024 39044 Z= 0.383 Chirality : 0.046 0.389 4249 Planarity : 0.005 0.062 4666 Dihedral : 19.669 177.722 5148 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.58 % Favored : 89.00 % Rotamer: Outliers : 4.74 % Allowed : 25.43 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.14), residues: 3081 helix: -0.33 (0.15), residues: 1121 sheet: -2.71 (0.22), residues: 459 loop : -3.29 (0.13), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 66 TYR 0.033 0.002 TYR M 106 PHE 0.027 0.002 PHE G 41 TRP 0.039 0.002 TRP J 77 HIS 0.010 0.002 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (28498) covalent geometry : angle 0.74165 / 0.38 (39044) hydrogen bonds : bond 0.06116 / 3.79 ( 878) hydrogen bonds : angle 5.39630 / 3.83 ( 2455) *********************** 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 674 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 548 time to evaluate : 0.823 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: A 16 GLN cc_start: 0.7101 (mp10) cc_final: 0.6350 (mm-40) REVERT: A 21 ASN cc_start: 0.7361 (t0) cc_final: 0.6842 (t0) REVERT: A 56 MET cc_start: 0.4604 (mtp) cc_final: 0.4125 (mtt) REVERT: A 66 PHE cc_start: 0.2204 (OUTLIER) cc_final: 0.1524 (m-80) REVERT: A 134 SER cc_start: 0.6613 (OUTLIER) cc_final: 0.6023 (t) REVERT: A 150 MET cc_start: 0.6017 (ptp) cc_final: 0.5741 (ptp) REVERT: A 184 ILE cc_start: 0.6183 (mm) cc_final: 0.5913 (mm) REVERT: B 143 LEU cc_start: 0.8365 (mt) cc_final: 0.7979 (mt) REVERT: B 264 TYR cc_start: 0.4822 (OUTLIER) cc_final: 0.4125 (m-80) REVERT: C 6 ARG cc_start: 0.5457 (mmm-85) cc_final: 0.5255 (tpp80) REVERT: C 64 ASP cc_start: 0.4412 (OUTLIER) cc_final: 0.3796 (m-30) REVERT: C 93 GLU cc_start: 0.7127 (pm20) cc_final: 0.6483 (tm-30) REVERT: C 134 SER cc_start: 0.6512 (OUTLIER) cc_final: 0.5726 (t) REVERT: C 150 MET cc_start: 0.7179 (ptm) cc_final: 0.6633 (ptm) REVERT: D 11 PHE cc_start: 0.5553 (t80) cc_final: 0.5207 (t80) REVERT: D 25 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.6309 (t0) REVERT: D 93 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7750 (mm-30) REVERT: D 107 TYR cc_start: 0.6560 (t80) cc_final: 0.6206 (t80) REVERT: D 141 MET cc_start: 0.7761 (mmt) cc_final: 0.7266 (mmt) REVERT: D 145 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7372 (m-70) REVERT: D 166 THR cc_start: 0.6209 (OUTLIER) cc_final: 0.5920 (p) REVERT: D 167 MET cc_start: 0.7157 (ttm) cc_final: 0.6848 (ttm) REVERT: E 66 PHE cc_start: 0.3012 (OUTLIER) cc_final: 0.2025 (m-80) REVERT: E 163 ASP cc_start: 0.3052 (OUTLIER) cc_final: 0.2797 (p0) REVERT: E 186 THR cc_start: 0.5334 (m) cc_final: 0.4831 (m) REVERT: E 204 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8160 (pp30) REVERT: F 53 PHE cc_start: 0.7797 (t80) cc_final: 0.7382 (t80) REVERT: F 66 PHE cc_start: 0.2928 (OUTLIER) cc_final: 0.1680 (t80) REVERT: F 131 LEU cc_start: 0.7223 (pt) cc_final: 0.7000 (pp) REVERT: F 188 PHE cc_start: 0.4966 (OUTLIER) cc_final: 0.3415 (m-80) REVERT: F 204 GLN cc_start: 0.8858 (pt0) cc_final: 0.8567 (pp30) REVERT: G 41 PHE cc_start: 0.8237 (t80) cc_final: 0.7939 (t80) REVERT: G 77 TRP cc_start: 0.6621 (t60) cc_final: 0.6265 (t60) REVERT: H 29 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: H 80 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6394 (tp) REVERT: H 87 TYR cc_start: 0.6043 (m-80) cc_final: 0.5810 (m-80) REVERT: H 215 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8056 (m-40) REVERT: H 235 GLU cc_start: 0.6235 (tm-30) cc_final: 0.5634 (tm-30) REVERT: H 420 LEU cc_start: 0.8933 (mp) cc_final: 0.8521 (mp) REVERT: H 563 TYR cc_start: 0.8251 (t80) cc_final: 0.7968 (t80) REVERT: I 56 MET cc_start: 0.8868 (mmm) cc_final: 0.8555 (mmm) REVERT: I 91 ASN cc_start: 0.7359 (m-40) cc_final: 0.7026 (m-40) REVERT: I 96 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7566 (mt-10) REVERT: I 98 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7648 (tp-100) REVERT: I 119 LYS cc_start: 0.8391 (mtmm) cc_final: 0.7922 (mtmm) REVERT: J 40 TYR cc_start: 0.8464 (m-80) cc_final: 0.8170 (m-10) REVERT: J 77 TRP cc_start: 0.7633 (t60) cc_final: 0.7172 (t60) REVERT: J 107 HIS cc_start: 0.6850 (m170) cc_final: 0.6386 (m-70) REVERT: M 47 LYS cc_start: 0.8070 (mttt) cc_final: 0.7574 (mptt) REVERT: M 116 MET cc_start: 0.7760 (mmt) cc_final: 0.7278 (tpp) REVERT: M 144 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6713 (mt-10) REVERT: M 178 TYR cc_start: 0.8513 (m-80) cc_final: 0.7766 (m-80) REVERT: N 89 GLN cc_start: 0.7198 (mt0) cc_final: 0.6816 (mt0) REVERT: N 123 GLU cc_start: 0.8086 (tp30) cc_final: 0.7630 (tm-30) REVERT: N 161 LEU cc_start: 0.4808 (OUTLIER) cc_final: 0.3796 (tt) REVERT: N 193 TYR cc_start: 0.7702 (t80) cc_final: 0.7334 (t80) outliers start: 126 outliers final: 68 residues processed: 623 average time/residue: 0.1757 time to fit residues: 177.3265 Evaluate side-chains 560 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 474 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 PHE 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 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 199 LEU 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 175 TYR Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE 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 215 SER Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 15 optimal weight: 0.0670 chunk 72 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 259 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 220 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 220 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 HIS N 89 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.159623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.141626 restraints weight = 68770.857| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 4.09 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 28498 Z= 0.160 Angle : 0.718 15.312 39044 Z= 0.368 Chirality : 0.045 0.385 4249 Planarity : 0.004 0.052 4666 Dihedral : 19.670 176.508 5145 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.58 % Favored : 89.03 % Rotamer: Outliers : 4.14 % Allowed : 25.73 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.14), residues: 3081 helix: -0.20 (0.15), residues: 1122 sheet: -2.82 (0.21), residues: 514 loop : -3.20 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 80 TYR 0.037 0.002 TYR F 107 PHE 0.020 0.002 PHE N 170 TRP 0.030 0.002 TRP J 77 HIS 0.010 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (28498) covalent geometry : angle 0.71841 / 0.37 (39044) hydrogen bonds : bond 0.06095 / 3.88 ( 878) hydrogen bonds : angle 5.33558 / 3.80 ( 2455) *********************** 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 620 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 510 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7496 (t0) cc_final: 0.6974 (t0) REVERT: A 56 MET cc_start: 0.4660 (mtp) cc_final: 0.4268 (mtt) REVERT: A 66 PHE cc_start: 0.1774 (OUTLIER) cc_final: 0.0920 (m-80) REVERT: A 150 MET cc_start: 0.6177 (ptp) cc_final: 0.5852 (ptp) REVERT: A 184 ILE cc_start: 0.6305 (mm) cc_final: 0.6036 (mm) REVERT: B 109 ILE cc_start: 0.7971 (mm) cc_final: 0.7739 (mm) REVERT: B 143 LEU cc_start: 0.8437 (mt) cc_final: 0.8009 (mt) REVERT: B 150 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6916 (ptm) REVERT: B 264 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.4261 (m-80) REVERT: C 6 ARG cc_start: 0.5594 (mmm-85) cc_final: 0.4937 (tpp80) REVERT: C 64 ASP cc_start: 0.4438 (OUTLIER) cc_final: 0.3820 (m-30) REVERT: C 93 GLU cc_start: 0.7164 (pm20) cc_final: 0.6505 (tm-30) REVERT: C 150 MET cc_start: 0.7019 (ptm) cc_final: 0.6323 (ptm) REVERT: C 166 THR cc_start: 0.7497 (t) cc_final: 0.7119 (p) REVERT: D 4 GLU cc_start: 0.6554 (pp20) cc_final: 0.6014 (pp20) REVERT: D 11 PHE cc_start: 0.5693 (t80) cc_final: 0.5335 (t80) REVERT: D 25 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6524 (t0) REVERT: D 93 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7712 (mm-30) REVERT: D 134 SER cc_start: 0.6654 (OUTLIER) cc_final: 0.6340 (t) REVERT: D 141 MET cc_start: 0.7816 (mmt) cc_final: 0.7616 (mmt) REVERT: D 166 THR cc_start: 0.6329 (OUTLIER) cc_final: 0.6039 (p) REVERT: D 167 MET cc_start: 0.7122 (ttm) cc_final: 0.6786 (ttm) REVERT: E 66 PHE cc_start: 0.3251 (OUTLIER) cc_final: 0.2652 (m-10) REVERT: E 94 LYS cc_start: 0.6127 (tttp) cc_final: 0.5064 (tmtt) REVERT: E 106 TYR cc_start: 0.7119 (m-80) cc_final: 0.6665 (t80) REVERT: E 163 ASP cc_start: 0.3364 (OUTLIER) cc_final: 0.2886 (p0) REVERT: E 197 ASN cc_start: 0.8383 (p0) cc_final: 0.8169 (p0) REVERT: E 204 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7940 (pp30) REVERT: E 220 GLN cc_start: 0.6850 (tt0) cc_final: 0.6473 (tt0) REVERT: F 53 PHE cc_start: 0.7802 (t80) cc_final: 0.7528 (t80) REVERT: F 66 PHE cc_start: 0.2928 (OUTLIER) cc_final: 0.1721 (t80) REVERT: F 167 MET cc_start: 0.5882 (ptp) cc_final: 0.5609 (ptt) REVERT: F 179 ARG cc_start: 0.4627 (ttt180) cc_final: 0.4363 (ttm-80) REVERT: F 181 HIS cc_start: 0.5442 (m170) cc_final: 0.5129 (m170) REVERT: F 204 GLN cc_start: 0.8710 (pt0) cc_final: 0.8408 (tm-30) REVERT: G 71 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8079 (mmm160) REVERT: H 2 ILE cc_start: 0.6181 (mm) cc_final: 0.5904 (mm) REVERT: H 215 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: H 235 GLU cc_start: 0.6182 (tm-30) cc_final: 0.5524 (tm-30) REVERT: H 288 MET cc_start: 0.8232 (mtm) cc_final: 0.7900 (pmm) REVERT: H 420 LEU cc_start: 0.8918 (mp) cc_final: 0.8516 (mp) REVERT: I 87 GLN cc_start: 0.7938 (pm20) cc_final: 0.7598 (tp-100) REVERT: I 88 ARG cc_start: 0.8441 (tmt170) cc_final: 0.8231 (tmt170) REVERT: I 91 ASN cc_start: 0.7410 (m-40) cc_final: 0.7091 (m-40) REVERT: I 96 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7553 (mt-10) REVERT: I 98 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7818 (tp-100) REVERT: I 119 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7898 (mtmm) REVERT: J 40 TYR cc_start: 0.8512 (m-80) cc_final: 0.8170 (m-10) REVERT: J 77 TRP cc_start: 0.7561 (t60) cc_final: 0.7272 (t60) REVERT: J 107 HIS cc_start: 0.7220 (m170) cc_final: 0.6763 (m-70) REVERT: M 47 LYS cc_start: 0.8171 (mttt) cc_final: 0.7634 (mptt) REVERT: M 66 PHE cc_start: 0.7130 (t80) cc_final: 0.6303 (t80) REVERT: M 116 MET cc_start: 0.7850 (mmt) cc_final: 0.7321 (tpp) REVERT: M 178 TYR cc_start: 0.8440 (m-80) cc_final: 0.8052 (m-80) REVERT: N 74 MET cc_start: 0.4704 (mpp) cc_final: 0.4343 (mpp) REVERT: N 89 GLN cc_start: 0.7574 (mt0) cc_final: 0.7196 (mt0) REVERT: N 123 GLU cc_start: 0.8115 (tp30) cc_final: 0.7645 (tm-30) REVERT: N 161 LEU cc_start: 0.5193 (OUTLIER) cc_final: 0.4187 (tt) REVERT: N 175 MET cc_start: 0.6052 (mtm) cc_final: 0.5494 (mtt) REVERT: N 193 TYR cc_start: 0.7730 (t80) cc_final: 0.7360 (t80) outliers start: 110 outliers final: 63 residues processed: 582 average time/residue: 0.1810 time to fit residues: 170.9174 Evaluate side-chains 537 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 460 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 PHE 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 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 212 HIS 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 32 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 163 ASP 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 66 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 192 LYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 220 optimal weight: 0.7980 chunk 153 optimal weight: 0.0980 chunk 166 optimal weight: 0.0670 chunk 277 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 267 optimal weight: 7.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN B 191 GLN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 233 ASN F 191 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN M 16 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.157795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.139811 restraints weight = 68787.702| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 4.08 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28498 Z= 0.158 Angle : 0.715 14.912 39044 Z= 0.365 Chirality : 0.045 0.387 4249 Planarity : 0.004 0.059 4666 Dihedral : 19.675 176.359 5145 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.80 % Favored : 89.78 % Rotamer: Outliers : 4.03 % Allowed : 26.30 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.14), residues: 3081 helix: -0.11 (0.15), residues: 1123 sheet: -2.72 (0.21), residues: 509 loop : -3.18 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 126 TYR 0.027 0.002 TYR N 26 PHE 0.023 0.002 PHE G 41 TRP 0.039 0.002 TRP H 146 HIS 0.013 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (28498) covalent geometry : angle 0.71458 / 0.36 (39044) hydrogen bonds : bond 0.05887 / 3.72 ( 878) hydrogen bonds : angle 5.29610 / 3.76 ( 2455) *********************** 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 623 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 516 time to evaluate : 0.761 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: A 21 ASN cc_start: 0.7670 (t0) cc_final: 0.7070 (t0) REVERT: A 56 MET cc_start: 0.4701 (mtp) cc_final: 0.4349 (mtt) REVERT: A 150 MET cc_start: 0.6272 (ptp) cc_final: 0.5992 (ptp) REVERT: A 184 ILE cc_start: 0.6488 (mm) cc_final: 0.6150 (mm) REVERT: B 109 ILE cc_start: 0.8078 (mm) cc_final: 0.7775 (mm) REVERT: B 143 LEU cc_start: 0.8080 (mt) cc_final: 0.7672 (mt) REVERT: B 264 TYR cc_start: 0.5234 (OUTLIER) cc_final: 0.4832 (m-80) REVERT: C 6 ARG cc_start: 0.5693 (mmm-85) cc_final: 0.5153 (tpp80) REVERT: C 64 ASP cc_start: 0.4463 (OUTLIER) cc_final: 0.3823 (m-30) REVERT: C 93 GLU cc_start: 0.7198 (pm20) cc_final: 0.6456 (tm-30) REVERT: C 103 CYS cc_start: 0.7731 (m) cc_final: 0.7471 (p) REVERT: C 134 SER cc_start: 0.6554 (OUTLIER) cc_final: 0.5918 (t) REVERT: C 150 MET cc_start: 0.7044 (ptm) cc_final: 0.6351 (ptm) REVERT: C 166 THR cc_start: 0.7514 (t) cc_final: 0.7189 (p) REVERT: C 177 LEU cc_start: 0.7680 (mp) cc_final: 0.7475 (mm) REVERT: C 204 GLN cc_start: 0.8121 (pt0) cc_final: 0.7890 (pp30) REVERT: C 270 ASP cc_start: 0.5781 (p0) cc_final: 0.5141 (p0) REVERT: D 11 PHE cc_start: 0.5938 (t80) cc_final: 0.5593 (t80) REVERT: D 25 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6589 (t0) REVERT: D 93 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7762 (mm-30) REVERT: D 134 SER cc_start: 0.6840 (OUTLIER) cc_final: 0.6526 (t) REVERT: D 141 MET cc_start: 0.7848 (mmt) cc_final: 0.7608 (mmt) REVERT: D 145 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7418 (m-70) REVERT: D 166 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6503 (p) REVERT: D 167 MET cc_start: 0.7280 (ttm) cc_final: 0.6836 (ttm) REVERT: E 66 PHE cc_start: 0.3038 (OUTLIER) cc_final: 0.2558 (m-80) REVERT: E 106 TYR cc_start: 0.7125 (m-80) cc_final: 0.6715 (t80) REVERT: E 163 ASP cc_start: 0.2994 (OUTLIER) cc_final: 0.2541 (p0) REVERT: E 197 ASN cc_start: 0.8356 (p0) cc_final: 0.8148 (p0) REVERT: E 204 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8144 (pp30) REVERT: E 206 LEU cc_start: 0.8050 (tp) cc_final: 0.7773 (tp) REVERT: F 53 PHE cc_start: 0.7649 (t80) cc_final: 0.7348 (t80) REVERT: F 167 MET cc_start: 0.5875 (ptp) cc_final: 0.5609 (ptt) REVERT: F 204 GLN cc_start: 0.8706 (pt0) cc_final: 0.8492 (tm-30) REVERT: H 148 GLU cc_start: 0.7574 (tp30) cc_final: 0.7312 (tp30) REVERT: H 215 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8076 (m-40) REVERT: H 235 GLU cc_start: 0.6429 (tm-30) cc_final: 0.5648 (tm-30) REVERT: H 288 MET cc_start: 0.8177 (mtm) cc_final: 0.7807 (pmm) REVERT: H 420 LEU cc_start: 0.8934 (mp) cc_final: 0.8537 (mp) REVERT: I 56 MET cc_start: 0.8658 (mmm) cc_final: 0.8401 (mmt) REVERT: I 88 ARG cc_start: 0.8467 (tmt170) cc_final: 0.8231 (tmt170) REVERT: I 91 ASN cc_start: 0.7459 (m-40) cc_final: 0.7112 (m-40) REVERT: I 96 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7708 (mt-10) REVERT: I 119 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7880 (mtmm) REVERT: J 77 TRP cc_start: 0.7394 (t60) cc_final: 0.6953 (t60) REVERT: J 107 HIS cc_start: 0.6975 (m170) cc_final: 0.6557 (m-70) REVERT: M 56 MET cc_start: 0.7725 (mmm) cc_final: 0.7035 (mmm) REVERT: M 66 PHE cc_start: 0.7240 (t80) cc_final: 0.6485 (t80) REVERT: M 116 MET cc_start: 0.7855 (mmt) cc_final: 0.7291 (tpp) REVERT: M 178 TYR cc_start: 0.8500 (m-80) cc_final: 0.7786 (m-80) REVERT: M 221 MET cc_start: 0.8496 (mmm) cc_final: 0.8241 (mmm) REVERT: N 80 SER cc_start: 0.8216 (m) cc_final: 0.7825 (t) REVERT: N 89 GLN cc_start: 0.7764 (mt0) cc_final: 0.6409 (mt0) REVERT: N 123 GLU cc_start: 0.8234 (tp30) cc_final: 0.7700 (tm-30) REVERT: N 161 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.4022 (tt) REVERT: N 175 MET cc_start: 0.5783 (mtm) cc_final: 0.5387 (mtt) REVERT: N 193 TYR cc_start: 0.7767 (t80) cc_final: 0.7510 (t80) outliers start: 107 outliers final: 73 residues processed: 576 average time/residue: 0.1651 time to fit residues: 156.0770 Evaluate side-chains 552 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 467 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL 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 134 SER 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 227 TYR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 212 HIS 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 32 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 100 GLN 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 273 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 175 TYR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 3 LEU 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 J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 215 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 63 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 198 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 212 HIS E 231 HIS F 35 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS H 41 ASN H 315 GLN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS I 33 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.140214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.120967 restraints weight = 67581.044| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.92 r_work: 0.3827 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 28498 Z= 0.314 Angle : 0.932 17.463 39044 Z= 0.474 Chirality : 0.053 0.438 4249 Planarity : 0.006 0.066 4666 Dihedral : 19.953 177.398 5143 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.78 % Favored : 87.80 % Rotamer: Outliers : 4.63 % Allowed : 26.64 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.14), residues: 3081 helix: -0.44 (0.15), residues: 1123 sheet: -2.89 (0.19), residues: 566 loop : -3.08 (0.14), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 48 TYR 0.035 0.003 TYR G 105 PHE 0.060 0.004 PHE C 112 TRP 0.039 0.003 TRP H 342 HIS 0.036 0.003 HIS H 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.31 (28498) covalent geometry : angle 0.93183 / 0.47 (39044) hydrogen bonds : bond 0.06906 / 4.36 ( 878) hydrogen bonds : angle 5.76150 / 4.10 ( 2455) *********************** 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 663 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 540 time to evaluate : 0.784 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 8 ASP cc_start: 0.7446 (m-30) cc_final: 0.7107 (m-30) REVERT: A 21 ASN cc_start: 0.8528 (t0) cc_final: 0.8142 (t0) REVERT: A 56 MET cc_start: 0.5486 (mtp) cc_final: 0.5203 (mtt) REVERT: A 141 MET cc_start: 0.7323 (mpp) cc_final: 0.7055 (mpp) REVERT: A 145 HIS cc_start: 0.8379 (m-70) cc_final: 0.8140 (m-70) REVERT: A 150 MET cc_start: 0.7812 (ptp) cc_final: 0.7544 (ptp) REVERT: A 184 ILE cc_start: 0.8084 (mm) cc_final: 0.7800 (mm) REVERT: A 187 HIS cc_start: 0.3247 (t-90) cc_final: 0.2957 (t-170) REVERT: B 8 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: B 90 GLU cc_start: 0.7184 (tp30) cc_final: 0.6755 (tm-30) REVERT: B 116 MET cc_start: 0.6965 (mpp) cc_final: 0.6630 (mpp) REVERT: B 143 LEU cc_start: 0.8275 (mt) cc_final: 0.7950 (mt) REVERT: C 56 MET cc_start: 0.4696 (ptt) cc_final: 0.4494 (ptt) REVERT: C 64 ASP cc_start: 0.4957 (OUTLIER) cc_final: 0.4103 (m-30) REVERT: C 68 ARG cc_start: 0.6884 (ttm170) cc_final: 0.6634 (ttm-80) REVERT: C 79 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: C 93 GLU cc_start: 0.7283 (pm20) cc_final: 0.6443 (tm-30) REVERT: C 150 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7380 (ptm) REVERT: C 166 THR cc_start: 0.7970 (t) cc_final: 0.7581 (p) REVERT: C 177 LEU cc_start: 0.8520 (mp) cc_final: 0.8318 (mm) REVERT: C 243 LEU cc_start: 0.8395 (tp) cc_final: 0.8111 (tp) REVERT: D 4 GLU cc_start: 0.7411 (pp20) cc_final: 0.7073 (pp20) REVERT: D 25 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6721 (t0) REVERT: D 134 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8101 (m) REVERT: D 141 MET cc_start: 0.7966 (mmt) cc_final: 0.7623 (mmt) REVERT: D 166 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7587 (p) REVERT: D 214 HIS cc_start: 0.6728 (m170) cc_final: 0.6482 (m170) REVERT: D 220 GLN cc_start: 0.7713 (tt0) cc_final: 0.7270 (tt0) REVERT: E 56 MET cc_start: 0.7289 (mmp) cc_final: 0.7012 (mmp) REVERT: E 66 PHE cc_start: 0.3730 (OUTLIER) cc_final: 0.3064 (m-10) REVERT: E 106 TYR cc_start: 0.7470 (m-80) cc_final: 0.6441 (t80) REVERT: E 186 THR cc_start: 0.6667 (m) cc_final: 0.6318 (m) REVERT: F 16 GLN cc_start: 0.6963 (tt0) cc_final: 0.6686 (tt0) REVERT: F 53 PHE cc_start: 0.7866 (t80) cc_final: 0.7110 (t80) REVERT: F 167 MET cc_start: 0.6021 (ptp) cc_final: 0.5728 (ptt) REVERT: F 204 GLN cc_start: 0.8817 (pt0) cc_final: 0.8549 (tm-30) REVERT: F 227 TYR cc_start: 0.5369 (m-80) cc_final: 0.4788 (m-80) REVERT: G 36 ILE cc_start: 0.9300 (pt) cc_final: 0.8911 (mm) REVERT: G 103 ILE cc_start: 0.7753 (mm) cc_final: 0.6209 (mm) REVERT: G 105 TYR cc_start: 0.8736 (t80) cc_final: 0.8456 (t80) REVERT: G 107 HIS cc_start: 0.7452 (m-70) cc_final: 0.6544 (m90) REVERT: H 47 ASP cc_start: 0.8087 (p0) cc_final: 0.7635 (p0) REVERT: H 148 GLU cc_start: 0.7815 (tp30) cc_final: 0.7370 (tp30) REVERT: H 215 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8115 (m-40) REVERT: H 235 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6174 (tm-30) REVERT: H 247 MET cc_start: 0.8344 (tmm) cc_final: 0.8083 (tmm) REVERT: I 12 TYR cc_start: 0.8046 (t80) cc_final: 0.7662 (t80) REVERT: I 65 LYS cc_start: 0.8986 (tttp) cc_final: 0.8653 (ttpp) REVERT: I 91 ASN cc_start: 0.8492 (m-40) cc_final: 0.8248 (m-40) REVERT: I 98 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8222 (tp40) REVERT: J 65 LYS cc_start: 0.8732 (tttp) cc_final: 0.8429 (tttp) REVERT: M 47 LYS cc_start: 0.8575 (mttt) cc_final: 0.8153 (mptt) REVERT: M 150 MET cc_start: 0.8223 (mtp) cc_final: 0.7825 (mtt) REVERT: M 178 TYR cc_start: 0.8833 (m-80) cc_final: 0.7864 (m-80) REVERT: M 209 MET cc_start: 0.8187 (ptt) cc_final: 0.7777 (ttp) REVERT: N 69 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: N 81 LEU cc_start: 0.8363 (tt) cc_final: 0.8149 (tt) REVERT: N 124 MET cc_start: 0.8504 (ptp) cc_final: 0.8185 (ptp) REVERT: N 161 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5182 (mp) REVERT: N 175 MET cc_start: 0.6509 (mtm) cc_final: 0.6149 (mtm) REVERT: N 193 TYR cc_start: 0.8183 (t80) cc_final: 0.7850 (t80) REVERT: N 202 ILE cc_start: 0.8382 (pt) cc_final: 0.7961 (tp) outliers start: 123 outliers final: 75 residues processed: 613 average time/residue: 0.1710 time to fit residues: 170.6816 Evaluate side-chains 547 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 460 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 134 SER 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 C residue 215 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 17 LEU 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 J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 98 VAL 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 34 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 294 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 220 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 191 GLN E 208 ASN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 GLN ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 HIS J 33 ASN J 120 ASN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.141861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.123257 restraints weight = 67185.654| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.89 r_work: 0.3867 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 28498 Z= 0.198 Angle : 0.809 15.426 39044 Z= 0.409 Chirality : 0.048 0.409 4249 Planarity : 0.005 0.107 4666 Dihedral : 19.960 175.189 5143 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.03 % Favored : 89.58 % Rotamer: Outliers : 3.31 % Allowed : 28.74 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.14), residues: 3081 helix: -0.40 (0.15), residues: 1124 sheet: -2.83 (0.20), residues: 540 loop : -3.05 (0.14), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 90 TYR 0.042 0.002 TYR M 175 PHE 0.046 0.002 PHE E 53 TRP 0.017 0.002 TRP H 146 HIS 0.008 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (28498) covalent geometry : angle 0.80933 / 0.41 (39044) hydrogen bonds : bond 0.06375 / 4.11 ( 878) hydrogen bonds : angle 5.59803 / 3.98 ( 2455) *********************** 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 603 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 515 time to evaluate : 0.917 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: A 8 ASP cc_start: 0.7354 (m-30) cc_final: 0.7007 (m-30) REVERT: A 65 ILE cc_start: 0.5415 (OUTLIER) cc_final: 0.5186 (pp) REVERT: A 141 MET cc_start: 0.7336 (mpp) cc_final: 0.7030 (mpp) REVERT: A 150 MET cc_start: 0.7530 (ptp) cc_final: 0.7262 (ptp) REVERT: A 184 ILE cc_start: 0.8083 (mm) cc_final: 0.7782 (mm) REVERT: B 35 GLN cc_start: 0.7727 (mp10) cc_final: 0.6606 (mp10) REVERT: B 90 GLU cc_start: 0.7109 (tp30) cc_final: 0.6685 (tm-30) REVERT: B 141 MET cc_start: 0.6917 (tpt) cc_final: 0.6653 (tpp) REVERT: B 143 LEU cc_start: 0.8064 (mt) cc_final: 0.7853 (mt) REVERT: C 6 ARG cc_start: 0.6478 (mmm-85) cc_final: 0.5981 (mmm160) REVERT: C 8 ASP cc_start: 0.7827 (m-30) cc_final: 0.7493 (m-30) REVERT: C 56 MET cc_start: 0.4974 (ptt) cc_final: 0.4604 (ptt) REVERT: C 64 ASP cc_start: 0.4900 (OUTLIER) cc_final: 0.4077 (m-30) REVERT: C 68 ARG cc_start: 0.6976 (ttm170) cc_final: 0.6692 (ttm-80) REVERT: C 93 GLU cc_start: 0.7359 (pm20) cc_final: 0.6566 (tm-30) REVERT: C 103 CYS cc_start: 0.8012 (m) cc_final: 0.7161 (p) REVERT: C 134 SER cc_start: 0.7955 (OUTLIER) cc_final: 0.7658 (m) REVERT: C 150 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7442 (ptm) REVERT: C 167 MET cc_start: 0.7449 (mtp) cc_final: 0.6925 (mtp) REVERT: C 177 LEU cc_start: 0.8267 (mp) cc_final: 0.8037 (mm) REVERT: D 25 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6599 (t0) REVERT: D 134 SER cc_start: 0.8143 (m) cc_final: 0.7853 (t) REVERT: D 141 MET cc_start: 0.8027 (mmt) cc_final: 0.7734 (mmt) REVERT: D 166 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7485 (p) REVERT: D 167 MET cc_start: 0.7860 (ttm) cc_final: 0.7547 (ttm) REVERT: D 172 THR cc_start: 0.8335 (m) cc_final: 0.8072 (p) REVERT: D 220 GLN cc_start: 0.7613 (tt0) cc_final: 0.7273 (tt0) REVERT: E 53 PHE cc_start: 0.6777 (t80) cc_final: 0.5956 (t80) REVERT: E 56 MET cc_start: 0.7232 (mmp) cc_final: 0.7009 (mmp) REVERT: E 66 PHE cc_start: 0.4101 (OUTLIER) cc_final: 0.3673 (m-10) REVERT: E 106 TYR cc_start: 0.7356 (m-80) cc_final: 0.6410 (t80) REVERT: E 186 THR cc_start: 0.6779 (m) cc_final: 0.6421 (m) REVERT: E 204 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8071 (pp30) REVERT: F 53 PHE cc_start: 0.7848 (t80) cc_final: 0.7218 (t80) REVERT: F 167 MET cc_start: 0.6016 (ptp) cc_final: 0.5730 (ptt) REVERT: F 204 GLN cc_start: 0.8880 (pt0) cc_final: 0.8551 (tm-30) REVERT: F 227 TYR cc_start: 0.5236 (m-80) cc_final: 0.4581 (m-80) REVERT: G 36 ILE cc_start: 0.9132 (pt) cc_final: 0.8701 (mm) REVERT: G 89 PHE cc_start: 0.4942 (OUTLIER) cc_final: 0.4646 (t80) REVERT: G 105 TYR cc_start: 0.8573 (t80) cc_final: 0.8251 (t80) REVERT: G 107 HIS cc_start: 0.7667 (m-70) cc_final: 0.6962 (m-70) REVERT: H 148 GLU cc_start: 0.7639 (tp30) cc_final: 0.7244 (tp30) REVERT: H 215 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8109 (m-40) REVERT: H 235 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6408 (tm-30) REVERT: H 271 THR cc_start: 0.8838 (m) cc_final: 0.8337 (p) REVERT: I 12 TYR cc_start: 0.7687 (t80) cc_final: 0.7293 (t80) REVERT: I 65 LYS cc_start: 0.8972 (tttp) cc_final: 0.8703 (ttpp) REVERT: I 91 ASN cc_start: 0.8464 (m-40) cc_final: 0.8112 (m-40) REVERT: I 98 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8210 (tp-100) REVERT: I 119 LYS cc_start: 0.8310 (mtpp) cc_final: 0.8078 (mtpp) REVERT: J 65 LYS cc_start: 0.8528 (tttp) cc_final: 0.8152 (tttp) REVERT: M 40 LEU cc_start: 0.7821 (mp) cc_final: 0.7499 (mm) REVERT: M 53 PHE cc_start: 0.8132 (t80) cc_final: 0.7729 (t80) REVERT: M 131 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8459 (tp) REVERT: M 178 TYR cc_start: 0.8846 (m-80) cc_final: 0.7829 (m-80) REVERT: M 209 MET cc_start: 0.8123 (ptt) cc_final: 0.7706 (ttp) REVERT: N 123 GLU cc_start: 0.8612 (tp30) cc_final: 0.7938 (tm-30) REVERT: N 124 MET cc_start: 0.8497 (ptp) cc_final: 0.7685 (ptp) REVERT: N 161 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.4758 (tt) REVERT: N 193 TYR cc_start: 0.8145 (t80) cc_final: 0.7886 (t80) outliers start: 88 outliers final: 59 residues processed: 572 average time/residue: 0.1669 time to fit residues: 156.4306 Evaluate side-chains 536 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 465 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain 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 264 TYR Chi-restraints excluded: chain G residue 89 PHE 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 254 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 363 MET 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 H residue 549 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU 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 J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 136 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 224 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 300 optimal weight: 0.0980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 ASN M 58 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.141138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.122565 restraints weight = 67749.936| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.80 r_work: 0.3860 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 28498 Z= 0.198 Angle : 0.811 15.528 39044 Z= 0.411 Chirality : 0.048 0.351 4249 Planarity : 0.005 0.102 4666 Dihedral : 19.949 175.304 5143 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.78 % Favored : 88.80 % Rotamer: Outliers : 3.31 % Allowed : 29.42 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.14), residues: 3081 helix: -0.42 (0.15), residues: 1123 sheet: -2.72 (0.20), residues: 556 loop : -2.95 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 449 TYR 0.040 0.002 TYR M 175 PHE 0.032 0.002 PHE D 53 TRP 0.015 0.002 TRP G 77 HIS 0.009 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (28498) covalent geometry : angle 0.81144 / 0.41 (39044) hydrogen bonds : bond 0.06211 / 4.00 ( 878) hydrogen bonds : angle 5.58780 / 3.97 ( 2455) *********************** 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 581 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 493 time to evaluate : 0.867 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 8 ASP cc_start: 0.7527 (m-30) cc_final: 0.7138 (m-30) REVERT: A 111 THR cc_start: 0.7383 (t) cc_final: 0.7093 (t) REVERT: A 141 MET cc_start: 0.7513 (mpp) cc_final: 0.7224 (mpp) REVERT: A 150 MET cc_start: 0.7485 (ptp) cc_final: 0.6939 (ptp) REVERT: A 184 ILE cc_start: 0.8136 (mm) cc_final: 0.7871 (mm) REVERT: A 243 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7670 (tp) REVERT: B 21 ASN cc_start: 0.7462 (t0) cc_final: 0.7183 (t0) REVERT: B 35 GLN cc_start: 0.7598 (mp10) cc_final: 0.6944 (mp10) REVERT: B 90 GLU cc_start: 0.7420 (tp30) cc_final: 0.6728 (tm-30) REVERT: B 116 MET cc_start: 0.7213 (mpp) cc_final: 0.6971 (mpp) REVERT: B 150 MET cc_start: 0.7748 (ptm) cc_final: 0.7205 (ptm) REVERT: C 6 ARG cc_start: 0.6761 (mmm-85) cc_final: 0.6198 (mmm160) REVERT: C 8 ASP cc_start: 0.7946 (m-30) cc_final: 0.7648 (m-30) REVERT: C 16 GLN cc_start: 0.6327 (mm-40) cc_final: 0.6126 (mm-40) REVERT: C 68 ARG cc_start: 0.6824 (ttm170) cc_final: 0.6568 (ttm-80) REVERT: C 93 GLU cc_start: 0.7302 (pm20) cc_final: 0.6730 (tm-30) REVERT: C 134 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7671 (m) REVERT: C 150 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7411 (ptm) REVERT: C 177 LEU cc_start: 0.8285 (mp) cc_final: 0.8060 (mm) REVERT: D 25 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6566 (t0) REVERT: D 134 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.7889 (t) REVERT: D 141 MET cc_start: 0.8071 (mmt) cc_final: 0.7761 (mmt) REVERT: D 166 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7621 (p) REVERT: D 167 MET cc_start: 0.7909 (ttm) cc_final: 0.7554 (ttm) REVERT: D 220 GLN cc_start: 0.7727 (tt0) cc_final: 0.7452 (tt0) REVERT: E 53 PHE cc_start: 0.6797 (t80) cc_final: 0.6393 (t80) REVERT: E 56 MET cc_start: 0.7338 (mmp) cc_final: 0.7078 (mmm) REVERT: E 66 PHE cc_start: 0.4237 (OUTLIER) cc_final: 0.3704 (m-10) REVERT: E 106 TYR cc_start: 0.7355 (m-80) cc_final: 0.6403 (t80) REVERT: E 186 THR cc_start: 0.7013 (m) cc_final: 0.6675 (m) REVERT: E 230 GLU cc_start: 0.6278 (mp0) cc_final: 0.6060 (mp0) REVERT: F 53 PHE cc_start: 0.7898 (t80) cc_final: 0.7260 (t80) REVERT: F 56 MET cc_start: 0.6611 (ptp) cc_final: 0.6369 (ptp) REVERT: F 167 MET cc_start: 0.6040 (ptp) cc_final: 0.5742 (ptt) REVERT: F 204 GLN cc_start: 0.8892 (pt0) cc_final: 0.8557 (tm-30) REVERT: F 227 TYR cc_start: 0.4998 (m-80) cc_final: 0.4623 (m-80) REVERT: G 36 ILE cc_start: 0.9246 (pt) cc_final: 0.8783 (mm) REVERT: G 89 PHE cc_start: 0.5022 (OUTLIER) cc_final: 0.4756 (t80) REVERT: G 103 ILE cc_start: 0.7560 (mm) cc_final: 0.6565 (mm) REVERT: G 105 TYR cc_start: 0.8436 (t80) cc_final: 0.8165 (t80) REVERT: G 107 HIS cc_start: 0.7640 (m-70) cc_final: 0.6920 (m-70) REVERT: H 59 ARG cc_start: 0.7408 (mtp-110) cc_final: 0.7207 (mtp-110) REVERT: H 148 GLU cc_start: 0.7716 (tp30) cc_final: 0.7339 (tp30) REVERT: H 215 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8212 (m-40) REVERT: H 235 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6478 (tm-30) REVERT: H 271 THR cc_start: 0.8959 (m) cc_final: 0.8413 (p) REVERT: I 12 TYR cc_start: 0.7524 (t80) cc_final: 0.7157 (t80) REVERT: I 65 LYS cc_start: 0.9005 (tttp) cc_final: 0.8713 (ttpp) REVERT: I 76 GLN cc_start: 0.8101 (mm110) cc_final: 0.7867 (mm-40) REVERT: I 91 ASN cc_start: 0.8474 (m-40) cc_final: 0.8138 (m-40) REVERT: I 98 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8055 (tp-100) REVERT: J 65 LYS cc_start: 0.8550 (tttp) cc_final: 0.8246 (tttp) REVERT: M 53 PHE cc_start: 0.8141 (t80) cc_final: 0.7719 (t80) REVERT: M 56 MET cc_start: 0.8411 (mmm) cc_final: 0.7661 (mmm) REVERT: M 167 MET cc_start: 0.8336 (mmp) cc_final: 0.7994 (tpp) REVERT: M 178 TYR cc_start: 0.8880 (m-80) cc_final: 0.7750 (m-80) REVERT: M 209 MET cc_start: 0.8152 (ptt) cc_final: 0.7706 (ttp) REVERT: M 221 MET cc_start: 0.8798 (mmm) cc_final: 0.8181 (mmm) REVERT: N 89 GLN cc_start: 0.8618 (mt0) cc_final: 0.7732 (mt0) REVERT: N 90 ARG cc_start: 0.8114 (tmm-80) cc_final: 0.7712 (ttp80) REVERT: N 123 GLU cc_start: 0.8600 (tp30) cc_final: 0.7963 (tm-30) REVERT: N 124 MET cc_start: 0.8529 (ptp) cc_final: 0.7861 (ptp) REVERT: N 161 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.4769 (tt) REVERT: N 175 MET cc_start: 0.6564 (mtm) cc_final: 0.6304 (mtm) REVERT: N 193 TYR cc_start: 0.8151 (t80) cc_final: 0.7921 (t80) REVERT: N 202 ILE cc_start: 0.8520 (pt) cc_final: 0.8071 (tp) outliers start: 88 outliers final: 64 residues processed: 544 average time/residue: 0.1623 time to fit residues: 143.7840 Evaluate side-chains 544 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 469 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 175 TYR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 89 PHE 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 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU 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 J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR 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 296 optimal weight: 4.9990 chunk 8 optimal weight: 0.0670 chunk 201 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN ** 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 = 0.4259 r_free = 0.4259 target = 0.140726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.122022 restraints weight = 67660.722| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.87 r_work: 0.3853 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 28498 Z= 0.190 Angle : 0.807 15.445 39044 Z= 0.407 Chirality : 0.047 0.355 4249 Planarity : 0.005 0.100 4666 Dihedral : 19.956 175.254 5143 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 26.39 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.13 % Favored : 89.39 % Rotamer: Outliers : 3.09 % Allowed : 29.80 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.14), residues: 3081 helix: -0.43 (0.15), residues: 1131 sheet: -2.65 (0.21), residues: 526 loop : -2.91 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 68 TYR 0.040 0.002 TYR M 175 PHE 0.042 0.002 PHE N 14 TRP 0.013 0.002 TRP H 146 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (28498) covalent geometry : angle 0.80736 / 0.41 (39044) hydrogen bonds : bond 0.06119 / 3.94 ( 878) hydrogen bonds : angle 5.53682 / 3.93 ( 2455) ********************** 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 572 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 490 time to evaluate : 0.945 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: A 8 ASP cc_start: 0.7563 (m-30) cc_final: 0.7211 (m-30) REVERT: A 111 THR cc_start: 0.7196 (t) cc_final: 0.6936 (t) REVERT: A 150 MET cc_start: 0.7446 (ptp) cc_final: 0.7159 (ptp) REVERT: B 21 ASN cc_start: 0.7537 (t0) cc_final: 0.7241 (t0) REVERT: B 35 GLN cc_start: 0.7506 (mp10) cc_final: 0.6929 (mp10) REVERT: B 90 GLU cc_start: 0.7364 (tp30) cc_final: 0.6750 (tm-30) REVERT: B 116 MET cc_start: 0.7354 (mpp) cc_final: 0.6614 (mpp) REVERT: C 6 ARG cc_start: 0.6771 (mmm-85) cc_final: 0.5348 (mmm160) REVERT: C 8 ASP cc_start: 0.7886 (m-30) cc_final: 0.7250 (m-30) REVERT: C 25 ASP cc_start: 0.7651 (m-30) cc_final: 0.7351 (m-30) REVERT: C 68 ARG cc_start: 0.6893 (ttm170) cc_final: 0.6654 (ttm-80) REVERT: C 93 GLU cc_start: 0.7360 (pm20) cc_final: 0.6783 (tm-30) REVERT: C 134 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7592 (m) REVERT: C 150 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7354 (ptm) REVERT: D 25 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6573 (t0) REVERT: D 66 PHE cc_start: 0.3775 (t80) cc_final: 0.2814 (t80) REVERT: D 134 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.7937 (t) REVERT: D 141 MET cc_start: 0.8104 (mmt) cc_final: 0.7711 (mmt) REVERT: D 160 GLU cc_start: 0.8269 (tp30) cc_final: 0.8045 (tm-30) REVERT: D 166 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7493 (p) REVERT: D 167 MET cc_start: 0.8001 (ttm) cc_final: 0.7651 (ttm) REVERT: D 220 GLN cc_start: 0.7697 (tt0) cc_final: 0.7408 (tt0) REVERT: E 53 PHE cc_start: 0.6779 (t80) cc_final: 0.6395 (t80) REVERT: E 56 MET cc_start: 0.7248 (mmp) cc_final: 0.6911 (mmm) REVERT: E 66 PHE cc_start: 0.4243 (OUTLIER) cc_final: 0.3744 (m-10) REVERT: E 106 TYR cc_start: 0.7454 (m-80) cc_final: 0.6396 (t80) REVERT: E 156 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7295 (mmmt) REVERT: E 186 THR cc_start: 0.7239 (m) cc_final: 0.6264 (m) REVERT: F 53 PHE cc_start: 0.7920 (t80) cc_final: 0.7188 (t80) REVERT: F 167 MET cc_start: 0.6026 (ptp) cc_final: 0.5736 (ptt) REVERT: F 204 GLN cc_start: 0.8881 (pt0) cc_final: 0.8560 (tm-30) REVERT: F 227 TYR cc_start: 0.4926 (m-80) cc_final: 0.4554 (m-80) REVERT: G 36 ILE cc_start: 0.9214 (pt) cc_final: 0.8957 (mm) REVERT: G 71 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7921 (ttm-80) REVERT: G 78 GLU cc_start: 0.7818 (tp30) cc_final: 0.7542 (tm-30) REVERT: G 105 TYR cc_start: 0.8516 (t80) cc_final: 0.8245 (t80) REVERT: G 107 HIS cc_start: 0.7623 (m-70) cc_final: 0.6890 (m-70) REVERT: H 59 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.7083 (mtp-110) REVERT: H 148 GLU cc_start: 0.7775 (tp30) cc_final: 0.7366 (tp30) REVERT: H 215 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8198 (m-40) REVERT: H 235 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6425 (tm-30) REVERT: H 271 THR cc_start: 0.8911 (m) cc_final: 0.8436 (p) REVERT: I 65 LYS cc_start: 0.9013 (tttp) cc_final: 0.8696 (ttpp) REVERT: I 76 GLN cc_start: 0.8045 (mm110) cc_final: 0.7785 (mm-40) REVERT: I 91 ASN cc_start: 0.8460 (m-40) cc_final: 0.8165 (m-40) REVERT: I 98 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7974 (tp-100) REVERT: J 65 LYS cc_start: 0.8587 (tttp) cc_final: 0.8184 (tttp) REVERT: J 74 GLN cc_start: 0.8230 (mp10) cc_final: 0.7846 (pm20) REVERT: M 53 PHE cc_start: 0.8171 (t80) cc_final: 0.7737 (t80) REVERT: M 56 MET cc_start: 0.8351 (mmm) cc_final: 0.7562 (mmm) REVERT: M 116 MET cc_start: 0.7918 (mmp) cc_final: 0.7270 (tpt) REVERT: M 167 MET cc_start: 0.8216 (mmp) cc_final: 0.7910 (tpp) REVERT: M 178 TYR cc_start: 0.8803 (m-80) cc_final: 0.7755 (m-80) REVERT: M 209 MET cc_start: 0.8282 (ptt) cc_final: 0.7878 (ttp) REVERT: M 221 MET cc_start: 0.8723 (mmm) cc_final: 0.8119 (mmm) REVERT: M 280 ARG cc_start: 0.7800 (mpt180) cc_final: 0.7521 (mmp-170) REVERT: N 89 GLN cc_start: 0.8523 (mt0) cc_final: 0.8006 (mt0) REVERT: N 123 GLU cc_start: 0.8524 (tp30) cc_final: 0.7939 (tm-30) REVERT: N 124 MET cc_start: 0.8522 (ptp) cc_final: 0.7777 (ptp) REVERT: N 136 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.4623 (t-90) REVERT: N 161 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.4756 (tt) REVERT: N 202 ILE cc_start: 0.8538 (pt) cc_final: 0.8079 (tp) outliers start: 82 outliers final: 61 residues processed: 534 average time/residue: 0.1631 time to fit residues: 142.9328 Evaluate side-chains 539 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 468 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 175 TYR Chi-restraints excluded: chain F residue 199 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 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR 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 285 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 231 optimal weight: 0.3980 chunk 175 optimal weight: 0.5980 chunk 205 optimal weight: 0.7980 chunk 243 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 283 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS J 91 ASN M 21 ASN M 63 HIS N 86 ASN ** 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 = 0.4262 r_free = 0.4262 target = 0.140660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.122300 restraints weight = 66876.201| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.80 r_work: 0.3868 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.7649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28498 Z= 0.187 Angle : 0.811 15.922 39044 Z= 0.409 Chirality : 0.047 0.364 4249 Planarity : 0.005 0.086 4666 Dihedral : 19.955 175.102 5143 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.55 % Favored : 89.03 % Rotamer: Outliers : 3.16 % Allowed : 30.17 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.14), residues: 3081 helix: -0.44 (0.15), residues: 1135 sheet: -2.55 (0.21), residues: 524 loop : -2.89 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 449 TYR 0.035 0.002 TYR M 175 PHE 0.035 0.002 PHE N 14 TRP 0.014 0.001 TRP J 77 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (28498) covalent geometry : angle 0.81087 / 0.41 (39044) hydrogen bonds : bond 0.06089 / 3.94 ( 878) hydrogen bonds : angle 5.52330 / 3.92 ( 2455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5567.73 seconds wall clock time: 96 minutes 59.08 seconds (5819.08 seconds total)