Starting phenix.real_space_refine on Sun Jul 5 10:09:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gan_29901/07_2026/8gan_29901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gan_29901/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gan_29901/07_2026/8gan_29901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gan_29901/07_2026/8gan_29901.map" model { file = "/net/cci-nas-00/data/ceres_data/8gan_29901/07_2026/8gan_29901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gan_29901/07_2026/8gan_29901.cif" } 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-dev-6108/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: 5.95, 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: 2.48 Conformation dependent library (CDL) restraints added in 962.3 milliseconds 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: 2.87 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: 4.91 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 38180 1.51 - 3.03: 767 3.03 - 4.54: 73 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=" 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 angle pdb=" C1' C K 38 " pdb=" N1 C K 38 " pdb=" C6 C K 38 " ideal model delta sigma weight residual 120.80 114.98 5.82 1.20e+00 6.94e-01 2.35e+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: 3559 0.050 - 0.100: 605 0.100 - 0.151: 79 0.151 - 0.201: 2 0.201 - 0.251: 4 Chirality restraints: 4249 Sorted by residual: chirality pdb=" C3' C K 22 " pdb=" C4' C K 22 " pdb=" O3' C K 22 " pdb=" C2' C K 22 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C2' C K 22 " pdb=" C3' C K 22 " pdb=" O2' C K 22 " pdb=" C1' C K 22 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4246 not shown) Planarity restraints: 4666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A K 6 " 0.031 2.00e-02 2.50e+03 1.38e-02 5.20e+00 pdb=" N9 A K 6 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A K 6 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A K 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A K 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A K 6 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A K 6 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A K 6 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A K 6 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C K 31 " 0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 C K 31 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C K 31 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C K 31 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C K 31 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C K 31 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C K 31 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C K 31 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C K 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 514 " -0.164 9.50e-02 1.11e+02 7.36e-02 3.43e+00 pdb=" NE ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 514 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 514 " -0.008 2.00e-02 2.50e+03 ... (remaining 4663 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 516 2.63 - 3.20: 23692 3.20 - 3.76: 47482 3.76 - 4.33: 65574 4.33 - 4.90: 104393 Nonbonded interactions: 241657 Sorted by model distance: nonbonded pdb=" N2 G K 30 " pdb=" O2 DC L 25 " model vdw 2.060 2.496 nonbonded pdb=" O THR A 148 " pdb=" O2' C K 31 " model vdw 2.135 3.040 nonbonded pdb=" O THR B 148 " pdb=" O2' U K 19 " model vdw 2.144 3.040 nonbonded pdb=" N2 G K 27 " pdb=" O2 DC L 28 " model vdw 2.161 2.496 nonbonded pdb=" O2 C K 43 " pdb=" N2 DG L 12 " model vdw 2.179 2.496 ... (remaining 241652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.440 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- 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= 0.216 Angle : 0.484 7.574 39044 Z= 0.355 Chirality : 0.038 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 0.00266 / 0.22 (28498) covalent geometry : angle 0.48372 / 0.36 (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 : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.2211 (OUTLIER) cc_final: 0.1998 (m-80) REVERT: A 147 ILE cc_start: 0.6579 (pt) cc_final: 0.6377 (pt) REVERT: C 66 PHE cc_start: 0.2217 (OUTLIER) cc_final: 0.1562 (m-80) REVERT: C 150 MET cc_start: 0.5846 (ptm) cc_final: 0.5400 (ptm) REVERT: D 53 PHE cc_start: 0.1101 (t80) cc_final: 0.0764 (t80) REVERT: D 153 THR cc_start: 0.3888 (OUTLIER) cc_final: 0.3656 (m) REVERT: E 273 LEU cc_start: 0.3861 (pp) cc_final: 0.3339 (tp) REVERT: F 66 PHE cc_start: 0.3434 (OUTLIER) cc_final: 0.1847 (t80) REVERT: F 214 HIS cc_start: 0.4919 (m-70) cc_final: 0.4654 (m-70) REVERT: G 21 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7742 (mt) REVERT: H 48 THR cc_start: 0.6527 (p) cc_final: 0.6289 (p) REVERT: H 73 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6718 (mtmm) REVERT: H 141 MET cc_start: 0.7798 (mpp) cc_final: 0.7449 (mmm) REVERT: H 155 CYS cc_start: 0.4920 (t) cc_final: 0.4203 (t) REVERT: H 505 PRO cc_start: 0.6413 (Cg_exo) cc_final: 0.6067 (Cg_endo) REVERT: H 549 HIS cc_start: 0.6907 (t-90) cc_final: 0.6589 (t-90) REVERT: N 36 ASN cc_start: 0.2953 (m-40) cc_final: 0.2447 (m110) REVERT: N 83 ILE cc_start: 0.6968 (pt) cc_final: 0.6509 (pt) outliers start: 81 outliers final: 10 residues processed: 1072 average time/residue: 0.2113 time to fit residues: 346.5031 Evaluate side-chains 592 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 577 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 HIS H 104 HIS 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 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.168374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.151843 restraints weight = 70526.251| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 4.11 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 28498 Z= 0.216 Angle : 0.807 12.791 39044 Z= 0.427 Chirality : 0.047 0.288 4249 Planarity : 0.006 0.058 4666 Dihedral : 19.725 178.224 5160 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.42 % Favored : 88.02 % Rotamer: Outliers : 4.44 % Allowed : 24.76 % Favored : 70.81 % 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: -3.32 (0.14), residues: 3081 helix: -0.43 (0.15), residues: 1101 sheet: -3.23 (0.22), residues: 439 loop : -3.33 (0.13), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 143 TYR 0.028 0.002 TYR J 40 PHE 0.023 0.002 PHE D 171 TRP 0.032 0.002 TRP J 77 HIS 0.011 0.002 HIS N 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (28498) covalent geometry : angle 0.80663 / 0.43 (39044) hydrogen bonds : bond 0.06930 / 4.24 ( 878) hydrogen bonds : angle 5.47772 / 3.82 ( 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 746 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 628 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7676 (tmm) cc_final: 0.7473 (tmm) REVERT: A 147 ILE cc_start: 0.7612 (pt) cc_final: 0.7404 (pt) REVERT: B 100 GLN cc_start: 0.7283 (tp40) cc_final: 0.7055 (tp40) REVERT: B 109 ILE cc_start: 0.8120 (mt) cc_final: 0.7756 (mt) REVERT: B 165 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7177 (mtt-85) REVERT: B 273 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7072 (pp) REVERT: C 40 LEU cc_start: 0.3620 (mt) cc_final: 0.3361 (mt) REVERT: C 41 VAL cc_start: 0.6539 (OUTLIER) cc_final: 0.6134 (t) REVERT: C 66 PHE cc_start: 0.1183 (OUTLIER) cc_final: 0.0850 (m-80) REVERT: C 150 MET cc_start: 0.7035 (ptm) cc_final: 0.6579 (ptp) REVERT: D 25 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6405 (t0) REVERT: D 62 HIS cc_start: 0.8218 (t-90) cc_final: 0.7761 (t70) REVERT: D 93 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7786 (mm-30) REVERT: D 107 TYR cc_start: 0.6164 (t80) cc_final: 0.5899 (t80) REVERT: D 150 MET cc_start: 0.6340 (ptp) cc_final: 0.6103 (ptp) REVERT: D 167 MET cc_start: 0.6698 (ttm) cc_final: 0.6330 (ttm) REVERT: E 4 GLU cc_start: 0.7493 (pm20) cc_final: 0.7133 (pm20) REVERT: E 11 PHE cc_start: 0.4486 (t80) cc_final: 0.4275 (t80) REVERT: E 93 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7295 (tm-30) REVERT: E 171 PHE cc_start: 0.7075 (m-80) cc_final: 0.6510 (m-80) REVERT: E 204 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8272 (pp30) REVERT: E 272 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6780 (t0) REVERT: F 56 MET cc_start: 0.6581 (ptp) cc_final: 0.6329 (ptp) REVERT: F 66 PHE cc_start: 0.3221 (OUTLIER) cc_final: 0.1975 (t80) REVERT: F 96 GLU cc_start: 0.7385 (tp30) cc_final: 0.7141 (tp30) REVERT: F 109 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8408 (mm) REVERT: G 21 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8396 (mt) REVERT: H 29 GLU cc_start: 0.8258 (tt0) cc_final: 0.7439 (tp30) REVERT: H 149 CYS cc_start: 0.5962 (OUTLIER) cc_final: 0.4838 (p) REVERT: H 249 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6849 (mp0) REVERT: H 420 LEU cc_start: 0.8832 (mp) cc_final: 0.8597 (mp) REVERT: I 40 TYR cc_start: 0.7647 (m-10) cc_final: 0.7310 (m-10) REVERT: I 91 ASN cc_start: 0.7017 (m-40) cc_final: 0.6589 (m-40) REVERT: I 98 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7390 (tp40) REVERT: J 77 TRP cc_start: 0.7033 (t60) cc_final: 0.6742 (t60) REVERT: M 64 ASP cc_start: 0.8139 (m-30) cc_final: 0.7742 (m-30) REVERT: M 178 TYR cc_start: 0.8321 (m-80) cc_final: 0.7962 (m-80) REVERT: N 36 ASN cc_start: 0.4993 (m-40) cc_final: 0.4705 (m-40) REVERT: N 50 LYS cc_start: 0.6912 (pttm) cc_final: 0.6601 (pttm) REVERT: N 64 ASN cc_start: 0.6823 (p0) cc_final: 0.6462 (p0) REVERT: N 94 LEU cc_start: 0.8824 (mt) cc_final: 0.8596 (mt) REVERT: N 161 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.3920 (tt) REVERT: N 179 LYS cc_start: 0.6773 (mtmm) cc_final: 0.6563 (pttp) outliers start: 118 outliers final: 49 residues processed: 695 average time/residue: 0.1879 time to fit residues: 206.8751 Evaluate side-chains 574 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 513 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 103 CYS 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 21 LEU 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 H residue 552 LEU Chi-restraints excluded: chain I residue 22 GLU 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 24 ILE 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 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: 0.9980 chunk 314 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 307 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 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 187 HIS A 234 ASN ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** 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 C 220 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 124 GLN ** E 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** E 233 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** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN H 313 ASN H 417 GLN ** 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 ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 GLN ** N 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.149766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.131409 restraints weight = 68604.270| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 4.04 r_work: 0.3983 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.161 28498 Z= 0.342 Angle : 0.932 22.014 39044 Z= 0.489 Chirality : 0.052 0.238 4249 Planarity : 0.007 0.070 4666 Dihedral : 20.023 177.923 5151 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.78 % Favored : 87.80 % Rotamer: Outliers : 5.53 % Allowed : 22.95 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.00 % 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: -3.36 (0.14), residues: 3081 helix: -0.66 (0.15), residues: 1121 sheet: -2.93 (0.21), residues: 475 loop : -3.32 (0.13), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG D 126 TYR 0.054 0.003 TYR F 178 PHE 0.038 0.003 PHE E 112 TRP 0.037 0.003 TRP J 77 HIS 0.018 0.002 HIS H 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.34 (28498) covalent geometry : angle 0.93157 / 0.49 (39044) hydrogen bonds : bond 0.07081 / 4.39 ( 878) hydrogen bonds : angle 5.71947 / 4.03 ( 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 734 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 587 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.6308 (OUTLIER) cc_final: 0.5910 (p) REVERT: A 56 MET cc_start: 0.4943 (mtp) cc_final: 0.4575 (mtt) REVERT: A 102 MET cc_start: 0.7861 (tmm) cc_final: 0.7600 (tmm) REVERT: A 147 ILE cc_start: 0.8493 (pt) cc_final: 0.8281 (pt) REVERT: A 199 LEU cc_start: 0.6959 (tp) cc_final: 0.6711 (tp) REVERT: B 109 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8451 (mt) REVERT: B 143 LEU cc_start: 0.8823 (mt) cc_final: 0.8483 (mt) REVERT: B 264 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: B 273 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7078 (pp) REVERT: C 23 ASP cc_start: 0.7603 (t0) cc_final: 0.7243 (t70) REVERT: C 56 MET cc_start: 0.3833 (OUTLIER) cc_final: 0.3430 (ptt) REVERT: C 64 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.4846 (m-30) REVERT: C 79 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: C 93 GLU cc_start: 0.7147 (pm20) cc_final: 0.6497 (tm-30) REVERT: D 4 GLU cc_start: 0.7586 (pp20) cc_final: 0.7382 (pp20) REVERT: D 8 ASP cc_start: 0.5197 (t0) cc_final: 0.4452 (t70) REVERT: D 25 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6510 (t0) REVERT: D 64 ASP cc_start: 0.4807 (OUTLIER) cc_final: 0.4511 (t0) REVERT: D 93 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7943 (mm-30) REVERT: D 166 THR cc_start: 0.7256 (OUTLIER) cc_final: 0.6977 (p) REVERT: D 167 MET cc_start: 0.7889 (ttm) cc_final: 0.7501 (ttm) REVERT: E 66 PHE cc_start: 0.3329 (OUTLIER) cc_final: 0.2943 (m-10) REVERT: E 166 THR cc_start: 0.4863 (OUTLIER) cc_final: 0.4662 (p) REVERT: E 167 MET cc_start: 0.3700 (ptm) cc_final: 0.3498 (ptp) REVERT: E 186 THR cc_start: 0.6331 (m) cc_final: 0.5871 (m) REVERT: E 204 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8085 (pp30) REVERT: E 206 LEU cc_start: 0.8456 (tp) cc_final: 0.7999 (tp) REVERT: E 220 GLN cc_start: 0.7440 (tt0) cc_final: 0.7218 (tt0) REVERT: E 235 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4868 (tt) REVERT: E 244 PHE cc_start: 0.6107 (m-80) cc_final: 0.5498 (m-10) REVERT: F 16 GLN cc_start: 0.6929 (tt0) cc_final: 0.6619 (tt0) REVERT: F 53 PHE cc_start: 0.7780 (t80) cc_final: 0.7300 (t80) REVERT: F 66 PHE cc_start: 0.3587 (OUTLIER) cc_final: 0.2330 (t80) REVERT: F 204 GLN cc_start: 0.8910 (pt0) cc_final: 0.8673 (pp30) REVERT: G 68 PHE cc_start: 0.5282 (m-80) cc_final: 0.4731 (m-80) REVERT: G 77 TRP cc_start: 0.6814 (t60) cc_final: 0.6406 (t60) REVERT: H 29 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: H 149 CYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5822 (p) REVERT: H 214 VAL cc_start: 0.8386 (t) cc_final: 0.8132 (t) REVERT: H 215 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: H 235 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6229 (tm-30) REVERT: H 420 LEU cc_start: 0.9152 (mp) cc_final: 0.8739 (mp) REVERT: I 12 TYR cc_start: 0.7403 (t80) cc_final: 0.7166 (t80) REVERT: I 91 ASN cc_start: 0.8337 (m-40) cc_final: 0.8068 (m-40) REVERT: I 96 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8259 (tt0) REVERT: J 77 TRP cc_start: 0.7782 (t60) cc_final: 0.7482 (t60) REVERT: M 53 PHE cc_start: 0.8123 (t80) cc_final: 0.7626 (t80) REVERT: M 64 ASP cc_start: 0.8313 (m-30) cc_final: 0.7905 (m-30) REVERT: M 106 TYR cc_start: 0.6762 (m-80) cc_final: 0.6501 (m-80) REVERT: M 150 MET cc_start: 0.8461 (mtp) cc_final: 0.8199 (mtp) REVERT: N 26 TYR cc_start: 0.8027 (m-80) cc_final: 0.7777 (m-80) REVERT: N 64 ASN cc_start: 0.7749 (p0) cc_final: 0.7491 (p0) REVERT: N 68 ASN cc_start: 0.7593 (m-40) cc_final: 0.6036 (m110) REVERT: N 89 GLN cc_start: 0.8472 (mt0) cc_final: 0.6630 (mm-40) REVERT: N 123 GLU cc_start: 0.8677 (tp30) cc_final: 0.7967 (tm-30) REVERT: N 124 MET cc_start: 0.8455 (ptp) cc_final: 0.7964 (ptp) REVERT: N 161 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.4944 (mp) REVERT: N 193 TYR cc_start: 0.7871 (t80) cc_final: 0.7267 (t80) outliers start: 147 outliers final: 68 residues processed: 668 average time/residue: 0.1871 time to fit residues: 199.7848 Evaluate side-chains 566 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 479 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 79 GLU 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 64 ASP 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 206 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 46 LEU 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 153 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 235 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 G residue 35 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 240 PHE 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 H residue 552 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 22 GLU 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 24 ILE 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 166 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 260 SER 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 98 VAL Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 161 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 291 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 235 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 251 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 220 GLN E 55 GLN E 208 ASN E 212 HIS ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS H 41 ASN H 156 ASN H 313 ASN ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.149932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.132569 restraints weight = 66766.489| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 3.87 r_work: 0.4011 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28498 Z= 0.187 Angle : 0.753 16.767 39044 Z= 0.389 Chirality : 0.045 0.234 4249 Planarity : 0.005 0.061 4666 Dihedral : 19.928 176.901 5145 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.90 % Favored : 89.65 % Rotamer: Outliers : 5.27 % Allowed : 24.76 % Favored : 69.98 % 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: -3.17 (0.14), residues: 3081 helix: -0.46 (0.15), residues: 1115 sheet: -2.82 (0.22), residues: 472 loop : -3.23 (0.13), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 224 TYR 0.024 0.002 TYR F 107 PHE 0.034 0.002 PHE D 53 TRP 0.031 0.002 TRP J 77 HIS 0.010 0.002 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (28498) covalent geometry : angle 0.75275 / 0.39 (39044) hydrogen bonds : bond 0.06465 / 4.07 ( 878) hydrogen bonds : angle 5.46999 / 3.88 ( 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 693 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 553 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.4893 (mtp) cc_final: 0.4661 (mtt) REVERT: A 72 ILE cc_start: 0.5998 (mm) cc_final: 0.5094 (mm) REVERT: A 124 GLN cc_start: 0.4307 (mm-40) cc_final: 0.3957 (mt0) REVERT: A 125 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7529 (m) REVERT: A 134 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.6882 (t) REVERT: A 150 MET cc_start: 0.6920 (ptp) cc_final: 0.6538 (ptp) REVERT: B 64 ASP cc_start: 0.5791 (OUTLIER) cc_final: 0.5282 (m-30) REVERT: B 143 LEU cc_start: 0.8478 (mt) cc_final: 0.8181 (mt) REVERT: B 264 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: C 6 ARG cc_start: 0.6169 (mmm-85) cc_final: 0.5172 (tpp80) REVERT: C 56 MET cc_start: 0.4042 (OUTLIER) cc_final: 0.3745 (ptt) REVERT: C 64 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.4745 (m-30) REVERT: C 93 GLU cc_start: 0.7168 (pm20) cc_final: 0.6487 (tm-30) REVERT: C 169 ARG cc_start: 0.7333 (mtp85) cc_final: 0.6997 (mtp85) REVERT: D 25 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6598 (t0) REVERT: D 64 ASP cc_start: 0.4679 (OUTLIER) cc_final: 0.4215 (t0) REVERT: D 93 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7848 (mm-30) REVERT: D 134 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.6973 (t) REVERT: D 167 MET cc_start: 0.7645 (ttm) cc_final: 0.7284 (ttm) REVERT: D 221 MET cc_start: 0.7435 (mtm) cc_final: 0.7053 (mtp) REVERT: D 256 GLU cc_start: 0.7194 (pm20) cc_final: 0.6962 (pm20) REVERT: E 94 LYS cc_start: 0.6412 (tttp) cc_final: 0.5362 (tmtt) REVERT: E 106 TYR cc_start: 0.7449 (m-80) cc_final: 0.6251 (t80) REVERT: E 131 LEU cc_start: 0.9000 (mp) cc_final: 0.8792 (tt) REVERT: E 163 ASP cc_start: 0.3210 (OUTLIER) cc_final: 0.2841 (p0) REVERT: E 186 THR cc_start: 0.6167 (m) cc_final: 0.5704 (m) REVERT: E 204 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: E 235 LEU cc_start: 0.5313 (OUTLIER) cc_final: 0.5088 (tt) REVERT: E 271 LYS cc_start: 0.5480 (OUTLIER) cc_final: 0.5112 (pptt) REVERT: F 53 PHE cc_start: 0.7797 (t80) cc_final: 0.7399 (t80) REVERT: F 66 PHE cc_start: 0.3746 (OUTLIER) cc_final: 0.2552 (t80) REVERT: G 41 PHE cc_start: 0.8604 (t80) cc_final: 0.8268 (t80) REVERT: G 77 TRP cc_start: 0.6928 (t60) cc_final: 0.6561 (t60) REVERT: H 80 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7278 (tp) REVERT: H 149 CYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5770 (p) REVERT: H 214 VAL cc_start: 0.8416 (t) cc_final: 0.8121 (t) REVERT: H 215 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7679 (m-40) REVERT: H 235 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6280 (tm-30) REVERT: H 261 GLU cc_start: 0.7884 (pm20) cc_final: 0.7607 (pm20) REVERT: H 420 LEU cc_start: 0.9098 (mp) cc_final: 0.8664 (mp) REVERT: I 56 MET cc_start: 0.9103 (mmm) cc_final: 0.8705 (mmt) REVERT: I 65 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8488 (tppp) REVERT: I 91 ASN cc_start: 0.8316 (m-40) cc_final: 0.8069 (m-40) REVERT: J 77 TRP cc_start: 0.7886 (t60) cc_final: 0.7358 (t60) REVERT: J 107 HIS cc_start: 0.7584 (m-70) cc_final: 0.7120 (m-70) REVERT: J 119 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7831 (mtmm) REVERT: M 40 LEU cc_start: 0.8041 (mm) cc_final: 0.7797 (mm) REVERT: M 53 PHE cc_start: 0.8083 (t80) cc_final: 0.7585 (t80) REVERT: M 64 ASP cc_start: 0.8225 (m-30) cc_final: 0.7880 (m-30) REVERT: M 150 MET cc_start: 0.8304 (mtp) cc_final: 0.7630 (mtt) REVERT: M 178 TYR cc_start: 0.8794 (m-80) cc_final: 0.8011 (m-80) REVERT: M 280 ARG cc_start: 0.7439 (mmp-170) cc_final: 0.7230 (mmp-170) REVERT: N 26 TYR cc_start: 0.7992 (m-80) cc_final: 0.7640 (m-80) REVERT: N 32 SER cc_start: 0.7115 (OUTLIER) cc_final: 0.5579 (m) REVERT: N 69 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: N 123 GLU cc_start: 0.8475 (tp30) cc_final: 0.7862 (tm-30) REVERT: N 147 CYS cc_start: 0.6844 (m) cc_final: 0.6349 (m) REVERT: N 161 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.4636 (tt) REVERT: N 193 TYR cc_start: 0.8012 (t80) cc_final: 0.7592 (t80) outliers start: 140 outliers final: 74 residues processed: 640 average time/residue: 0.1827 time to fit residues: 188.3806 Evaluate side-chains 590 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 494 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 125 VAL 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 265 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 242 SER 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 56 MET Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 148 THR 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 C residue 258 VAL 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 64 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain E residue 32 ILE 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 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 66 PHE 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 17 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 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 301 ILE Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 503 SER Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 65 LYS 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 J residue 119 LYS 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 72 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 15 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 220 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 310 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN E 208 ASN E 233 ASN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN J 87 GLN M 16 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.148843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.130700 restraints weight = 67688.014| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.96 r_work: 0.3984 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5965 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= 0.181 Angle : 0.733 15.513 39044 Z= 0.379 Chirality : 0.045 0.238 4249 Planarity : 0.005 0.095 4666 Dihedral : 19.911 176.705 5145 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.48 % Favored : 89.09 % Rotamer: Outliers : 4.51 % Allowed : 26.71 % Favored : 68.77 % 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: -3.13 (0.14), residues: 3081 helix: -0.40 (0.15), residues: 1114 sheet: -2.93 (0.20), residues: 516 loop : -3.16 (0.14), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG N 90 TYR 0.031 0.002 TYR M 106 PHE 0.022 0.002 PHE M 261 TRP 0.031 0.002 TRP H 146 HIS 0.008 0.001 HIS H 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (28498) covalent geometry : angle 0.73302 / 0.38 (39044) hydrogen bonds : bond 0.06180 / 3.91 ( 878) hydrogen bonds : angle 5.39684 / 3.82 ( 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 648 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 528 time to evaluate : 0.925 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 16 GLN cc_start: 0.7202 (mm110) cc_final: 0.6941 (mt0) REVERT: A 21 ASN cc_start: 0.8004 (t0) cc_final: 0.7715 (t0) REVERT: A 66 PHE cc_start: 0.1787 (OUTLIER) cc_final: 0.0960 (m-80) REVERT: A 124 GLN cc_start: 0.4416 (mm-40) cc_final: 0.4117 (mt0) REVERT: A 141 MET cc_start: 0.7508 (mpp) cc_final: 0.7230 (mpp) REVERT: B 64 ASP cc_start: 0.5797 (OUTLIER) cc_final: 0.5269 (m-30) REVERT: B 143 LEU cc_start: 0.8329 (mt) cc_final: 0.8048 (mt) REVERT: B 264 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.5347 (m-80) REVERT: C 6 ARG cc_start: 0.6079 (mmm-85) cc_final: 0.5264 (tpp80) REVERT: C 56 MET cc_start: 0.4018 (OUTLIER) cc_final: 0.3706 (ptt) REVERT: C 64 ASP cc_start: 0.5695 (OUTLIER) cc_final: 0.4672 (m-30) REVERT: C 93 GLU cc_start: 0.7238 (pm20) cc_final: 0.6532 (tm-30) REVERT: C 103 CYS cc_start: 0.7663 (m) cc_final: 0.7032 (p) REVERT: C 270 ASP cc_start: 0.5805 (p0) cc_final: 0.5130 (p0) REVERT: D 4 GLU cc_start: 0.7178 (pp20) cc_final: 0.6911 (pp20) REVERT: D 25 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6661 (t0) REVERT: D 36 THR cc_start: 0.6598 (p) cc_final: 0.6112 (t) REVERT: D 64 ASP cc_start: 0.4166 (OUTLIER) cc_final: 0.3964 (t0) REVERT: D 93 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7842 (mm-30) REVERT: D 134 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7301 (t) REVERT: D 141 MET cc_start: 0.7926 (mmt) cc_final: 0.7679 (mmt) REVERT: D 166 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.7059 (p) REVERT: D 221 MET cc_start: 0.7682 (mtm) cc_final: 0.7326 (mtp) REVERT: E 66 PHE cc_start: 0.3942 (OUTLIER) cc_final: 0.3386 (m-10) REVERT: E 94 LYS cc_start: 0.6623 (tttp) cc_final: 0.5831 (tmtt) REVERT: E 106 TYR cc_start: 0.7466 (m-80) cc_final: 0.6687 (t80) REVERT: E 163 ASP cc_start: 0.3261 (OUTLIER) cc_final: 0.2789 (p0) REVERT: E 186 THR cc_start: 0.6300 (m) cc_final: 0.5862 (m) REVERT: E 204 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8216 (pp30) REVERT: E 235 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5112 (tt) REVERT: F 66 PHE cc_start: 0.3891 (OUTLIER) cc_final: 0.2714 (t80) REVERT: F 68 ARG cc_start: 0.2489 (mmt180) cc_final: 0.2119 (mmt180) REVERT: F 204 GLN cc_start: 0.8401 (pp30) cc_final: 0.8030 (pp30) REVERT: G 77 TRP cc_start: 0.7362 (t60) cc_final: 0.7087 (t60) REVERT: G 78 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7191 (tm-30) REVERT: H 29 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: H 59 ARG cc_start: 0.7458 (mtp-110) cc_final: 0.6765 (mtp-110) REVERT: H 80 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7297 (tp) REVERT: H 149 CYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5612 (p) REVERT: H 215 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7700 (m-40) REVERT: H 235 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6353 (tm-30) REVERT: H 261 GLU cc_start: 0.8005 (pm20) cc_final: 0.7716 (pm20) REVERT: H 271 THR cc_start: 0.8777 (m) cc_final: 0.8282 (p) REVERT: H 420 LEU cc_start: 0.9114 (mp) cc_final: 0.8668 (mp) REVERT: I 38 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: I 56 MET cc_start: 0.9131 (mmm) cc_final: 0.8851 (mmt) REVERT: I 87 GLN cc_start: 0.8368 (tp40) cc_final: 0.8050 (tp-100) REVERT: I 91 ASN cc_start: 0.8297 (m-40) cc_final: 0.8046 (m-40) REVERT: J 107 HIS cc_start: 0.7667 (m-70) cc_final: 0.7117 (m-70) REVERT: M 2 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7293 (m) REVERT: M 53 PHE cc_start: 0.8121 (t80) cc_final: 0.7605 (t80) REVERT: M 66 PHE cc_start: 0.7353 (t80) cc_final: 0.6909 (t80) REVERT: M 144 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7457 (mt-10) REVERT: M 150 MET cc_start: 0.8125 (mtp) cc_final: 0.7820 (mtp) REVERT: M 178 TYR cc_start: 0.8755 (m-80) cc_final: 0.8066 (m-80) REVERT: M 280 ARG cc_start: 0.7524 (mmp-170) cc_final: 0.7217 (mmp-170) REVERT: N 25 SER cc_start: 0.8845 (p) cc_final: 0.8558 (m) REVERT: N 32 SER cc_start: 0.7070 (OUTLIER) cc_final: 0.5582 (m) REVERT: N 123 GLU cc_start: 0.8480 (tp30) cc_final: 0.7842 (tm-30) REVERT: N 147 CYS cc_start: 0.6683 (m) cc_final: 0.6075 (m) REVERT: N 161 LEU cc_start: 0.5814 (OUTLIER) cc_final: 0.4683 (tt) REVERT: N 193 TYR cc_start: 0.8091 (t80) cc_final: 0.7658 (t80) outliers start: 120 outliers final: 67 residues processed: 603 average time/residue: 0.1798 time to fit residues: 174.8791 Evaluate side-chains 578 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 489 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 PHE 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 265 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 153 THR 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 242 SER 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 45 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 215 SER 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 64 ASP 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 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 134 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 264 TYR 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 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 51 VAL Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 38 ASP 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 47 THR Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain N residue 32 SER 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 161 LEU Chi-restraints excluded: chain N residue 171 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 277 optimal weight: 8.9990 chunk 11 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 267 optimal weight: 8.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 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** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 220 GLN E 208 ASN F 35 GLN ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.147031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.128660 restraints weight = 67707.745| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.95 r_work: 0.3957 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28498 Z= 0.183 Angle : 0.727 14.800 39044 Z= 0.375 Chirality : 0.045 0.436 4249 Planarity : 0.005 0.123 4666 Dihedral : 19.931 175.936 5144 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.42 % Favored : 89.16 % Rotamer: Outliers : 4.78 % Allowed : 26.41 % Favored : 68.81 % 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: -0.32 (0.15), residues: 1120 sheet: -2.97 (0.19), residues: 546 loop : -3.14 (0.14), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG N 90 TYR 0.036 0.002 TYR N 26 PHE 0.028 0.002 PHE F 53 TRP 0.035 0.002 TRP H 146 HIS 0.008 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (28498) covalent geometry : angle 0.72745 / 0.38 (39044) hydrogen bonds : bond 0.06086 / 3.84 ( 878) hydrogen bonds : angle 5.33085 / 3.77 ( 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 654 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 527 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7272 (mm110) cc_final: 0.6979 (mt0) REVERT: A 21 ASN cc_start: 0.8117 (t0) cc_final: 0.7838 (t0) REVERT: A 124 GLN cc_start: 0.4452 (mm-40) cc_final: 0.3866 (mt0) REVERT: A 125 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.7840 (m) REVERT: A 141 MET cc_start: 0.7305 (mpp) cc_final: 0.6974 (mpp) REVERT: B 8 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: B 64 ASP cc_start: 0.5912 (OUTLIER) cc_final: 0.5323 (m-30) REVERT: B 66 PHE cc_start: 0.3329 (OUTLIER) cc_final: 0.2774 (m-80) REVERT: B 143 LEU cc_start: 0.8264 (mt) cc_final: 0.8010 (mt) REVERT: B 264 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5639 (m-10) REVERT: C 6 ARG cc_start: 0.6444 (mmm-85) cc_final: 0.5963 (tpp80) REVERT: C 41 VAL cc_start: 0.7959 (t) cc_final: 0.7518 (p) REVERT: C 68 ARG cc_start: 0.6743 (ttm170) cc_final: 0.6466 (ttm-80) REVERT: C 93 GLU cc_start: 0.7108 (pm20) cc_final: 0.6428 (tm-30) REVERT: C 103 CYS cc_start: 0.7745 (m) cc_final: 0.7094 (p) REVERT: C 270 ASP cc_start: 0.5947 (p0) cc_final: 0.5300 (p0) REVERT: D 25 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6484 (t0) REVERT: D 93 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7913 (mm-30) REVERT: D 106 TYR cc_start: 0.6885 (m-80) cc_final: 0.6544 (m-80) REVERT: D 134 SER cc_start: 0.7955 (OUTLIER) cc_final: 0.7558 (t) REVERT: D 141 MET cc_start: 0.7997 (mmt) cc_final: 0.7690 (mmt) REVERT: D 167 MET cc_start: 0.7771 (ttm) cc_final: 0.7368 (ttm) REVERT: D 220 GLN cc_start: 0.7119 (tt0) cc_final: 0.6663 (tt0) REVERT: D 221 MET cc_start: 0.7794 (mtm) cc_final: 0.7456 (mtp) REVERT: E 41 VAL cc_start: 0.7400 (t) cc_final: 0.7092 (p) REVERT: E 66 PHE cc_start: 0.4472 (OUTLIER) cc_final: 0.3617 (m-10) REVERT: E 94 LYS cc_start: 0.6646 (tttp) cc_final: 0.5869 (tmtt) REVERT: E 106 TYR cc_start: 0.7445 (m-80) cc_final: 0.6688 (t80) REVERT: E 186 THR cc_start: 0.6467 (m) cc_final: 0.6060 (m) REVERT: E 213 ASP cc_start: 0.7308 (t0) cc_final: 0.6872 (p0) REVERT: F 53 PHE cc_start: 0.7833 (t80) cc_final: 0.7445 (t80) REVERT: F 66 PHE cc_start: 0.3820 (OUTLIER) cc_final: 0.2644 (t80) REVERT: G 77 TRP cc_start: 0.7278 (t60) cc_final: 0.7070 (t60) REVERT: G 78 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7046 (tm-30) REVERT: H 29 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: H 59 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.6812 (mtp-110) REVERT: H 80 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7303 (tp) REVERT: H 148 GLU cc_start: 0.7739 (tp30) cc_final: 0.7333 (tp30) REVERT: H 149 CYS cc_start: 0.5741 (OUTLIER) cc_final: 0.5349 (p) REVERT: H 215 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.7857 (m-40) REVERT: H 235 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6385 (tm-30) REVERT: H 257 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7872 (tp) REVERT: H 261 GLU cc_start: 0.8185 (pm20) cc_final: 0.7953 (pm20) REVERT: H 271 THR cc_start: 0.8860 (m) cc_final: 0.8331 (p) REVERT: H 344 GLU cc_start: 0.7650 (tp30) cc_final: 0.7335 (tp30) REVERT: H 420 LEU cc_start: 0.9122 (mp) cc_final: 0.8673 (mp) REVERT: I 12 TYR cc_start: 0.7361 (t80) cc_final: 0.7049 (t80) REVERT: I 38 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: I 56 MET cc_start: 0.9108 (mmm) cc_final: 0.8813 (mmt) REVERT: I 87 GLN cc_start: 0.8227 (tp40) cc_final: 0.7940 (tp-100) REVERT: I 113 PHE cc_start: 0.8152 (m-80) cc_final: 0.7904 (m-80) REVERT: J 77 TRP cc_start: 0.7954 (t60) cc_final: 0.7475 (t60) REVERT: J 107 HIS cc_start: 0.7691 (m-70) cc_final: 0.7027 (m-70) REVERT: M 53 PHE cc_start: 0.8211 (t80) cc_final: 0.7683 (t80) REVERT: M 66 PHE cc_start: 0.7613 (t80) cc_final: 0.6878 (t80) REVERT: M 144 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7502 (mt-10) REVERT: M 178 TYR cc_start: 0.8853 (m-80) cc_final: 0.8003 (m-80) REVERT: M 186 THR cc_start: 0.5928 (OUTLIER) cc_final: 0.5727 (m) REVERT: M 280 ARG cc_start: 0.7471 (mmp-170) cc_final: 0.7264 (mmp-170) REVERT: N 36 ASN cc_start: 0.5884 (m-40) cc_final: 0.5330 (m-40) REVERT: N 69 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: N 123 GLU cc_start: 0.8519 (tp30) cc_final: 0.7918 (tm-30) REVERT: N 125 PHE cc_start: 0.7845 (t80) cc_final: 0.7438 (t80) REVERT: N 147 CYS cc_start: 0.6308 (m) cc_final: 0.5907 (m) REVERT: N 161 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.4709 (tt) REVERT: N 193 TYR cc_start: 0.8206 (t80) cc_final: 0.7770 (t80) outliers start: 127 outliers final: 76 residues processed: 605 average time/residue: 0.1793 time to fit residues: 176.7730 Evaluate side-chains 592 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 498 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 THR 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 242 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 250 VAL 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 77 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 201 LEU 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 134 SER 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 199 LEU Chi-restraints excluded: chain E residue 264 TYR 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 175 TYR Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 192 LYS 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 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 38 ASP 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 45 SER Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 80 ARG 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 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 161 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 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** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 220 GLN E 55 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 87 GLN M 58 GLN ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 89 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.140119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.122247 restraints weight = 66545.869| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.73 r_work: 0.3861 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28498 Z= 0.226 Angle : 0.781 15.435 39044 Z= 0.403 Chirality : 0.047 0.254 4249 Planarity : 0.005 0.090 4666 Dihedral : 20.019 176.120 5144 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.04 % Favored : 88.54 % Rotamer: Outliers : 4.93 % Allowed : 26.82 % Favored : 68.25 % 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: -3.01 (0.14), residues: 3081 helix: -0.36 (0.15), residues: 1123 sheet: -2.89 (0.20), residues: 552 loop : -3.02 (0.14), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 165 TYR 0.029 0.002 TYR J 40 PHE 0.033 0.002 PHE G 18 TRP 0.045 0.002 TRP H 146 HIS 0.012 0.002 HIS G 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (28498) covalent geometry : angle 0.78066 / 0.40 (39044) hydrogen bonds : bond 0.06225 / 3.95 ( 878) hydrogen bonds : angle 5.39680 / 3.81 ( 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 668 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 537 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7177 (m-30) cc_final: 0.6829 (m-30) REVERT: A 16 GLN cc_start: 0.7366 (mm110) cc_final: 0.7094 (mt0) REVERT: A 56 MET cc_start: 0.5548 (mtp) cc_final: 0.5308 (mmm) REVERT: A 145 HIS cc_start: 0.7652 (m90) cc_final: 0.7437 (m90) REVERT: A 150 MET cc_start: 0.7356 (ptp) cc_final: 0.6919 (ptp) REVERT: B 8 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: B 29 LEU cc_start: 0.8762 (pp) cc_final: 0.8516 (pp) REVERT: B 64 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5438 (m-30) REVERT: B 90 GLU cc_start: 0.7245 (tp30) cc_final: 0.6677 (tm-30) REVERT: B 141 MET cc_start: 0.6558 (tpp) cc_final: 0.6273 (mmt) REVERT: B 143 LEU cc_start: 0.8289 (mt) cc_final: 0.7979 (mt) REVERT: C 93 GLU cc_start: 0.7391 (pm20) cc_final: 0.6476 (tm-30) REVERT: C 270 ASP cc_start: 0.6196 (p0) cc_final: 0.5374 (p0) REVERT: D 25 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6448 (t0) REVERT: D 134 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.7805 (t) REVERT: D 141 MET cc_start: 0.7935 (mmt) cc_final: 0.7548 (mmt) REVERT: D 166 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7417 (p) REVERT: D 167 MET cc_start: 0.7858 (ttm) cc_final: 0.7511 (ttm) REVERT: D 178 TYR cc_start: 0.7529 (m-10) cc_final: 0.7224 (m-80) REVERT: D 220 GLN cc_start: 0.7485 (tt0) cc_final: 0.7038 (tt0) REVERT: D 221 MET cc_start: 0.7888 (mtm) cc_final: 0.7669 (mtp) REVERT: D 271 LYS cc_start: 0.8022 (pttm) cc_final: 0.7735 (pttm) REVERT: E 66 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.3864 (m-10) REVERT: E 94 LYS cc_start: 0.6899 (tttp) cc_final: 0.6137 (tmtt) REVERT: E 106 TYR cc_start: 0.7490 (m-80) cc_final: 0.6448 (t80) REVERT: E 186 THR cc_start: 0.6938 (m) cc_final: 0.6581 (m) REVERT: E 213 ASP cc_start: 0.7187 (t0) cc_final: 0.6824 (p0) REVERT: E 271 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5624 (ptpt) REVERT: F 178 TYR cc_start: 0.6369 (m-80) cc_final: 0.6043 (m-80) REVERT: G 71 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8419 (mmm160) REVERT: G 78 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7099 (tm-30) REVERT: G 107 HIS cc_start: 0.7540 (m-70) cc_final: 0.6649 (m90) REVERT: H 29 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: H 59 ARG cc_start: 0.7448 (mtp-110) cc_final: 0.6669 (mtm-85) REVERT: H 87 TYR cc_start: 0.6390 (m-80) cc_final: 0.5897 (m-80) REVERT: H 148 GLU cc_start: 0.7722 (tp30) cc_final: 0.7105 (tp30) REVERT: H 215 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8196 (m-40) REVERT: H 235 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6159 (tm-30) REVERT: H 271 THR cc_start: 0.8907 (m) cc_final: 0.8464 (p) REVERT: H 324 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8008 (mmmt) REVERT: H 420 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8772 (mp) REVERT: H 579 PHE cc_start: 0.8273 (t80) cc_final: 0.8056 (t80) REVERT: I 67 GLU cc_start: 0.8957 (pt0) cc_final: 0.8600 (pt0) REVERT: I 68 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: I 87 GLN cc_start: 0.8402 (tp40) cc_final: 0.8038 (tp-100) REVERT: I 91 ASN cc_start: 0.8447 (m-40) cc_final: 0.8215 (m-40) REVERT: I 113 PHE cc_start: 0.8156 (m-80) cc_final: 0.7898 (m-80) REVERT: J 119 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7708 (mtmm) REVERT: M 53 PHE cc_start: 0.8306 (t80) cc_final: 0.7732 (t80) REVERT: M 116 MET cc_start: 0.8059 (mmt) cc_final: 0.7382 (tpp) REVERT: M 150 MET cc_start: 0.8436 (mtp) cc_final: 0.7904 (mtt) REVERT: M 178 TYR cc_start: 0.8966 (m-80) cc_final: 0.7940 (m-80) REVERT: M 186 THR cc_start: 0.6062 (OUTLIER) cc_final: 0.5837 (m) REVERT: M 280 ARG cc_start: 0.7550 (mmp-170) cc_final: 0.7252 (mmp-170) REVERT: N 25 SER cc_start: 0.8904 (p) cc_final: 0.8687 (m) REVERT: N 36 ASN cc_start: 0.6056 (m-40) cc_final: 0.5652 (m-40) REVERT: N 69 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: N 123 GLU cc_start: 0.8567 (tp30) cc_final: 0.7917 (tm-30) REVERT: N 125 PHE cc_start: 0.7963 (t80) cc_final: 0.7599 (t80) REVERT: N 136 HIS cc_start: 0.6081 (OUTLIER) cc_final: 0.4618 (t70) REVERT: N 161 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.4841 (tt) REVERT: N 193 TYR cc_start: 0.8288 (t80) cc_final: 0.7920 (t80) outliers start: 131 outliers final: 83 residues processed: 608 average time/residue: 0.1822 time to fit residues: 179.3368 Evaluate side-chains 588 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 489 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 265 LEU Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 64 ASP 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 187 HIS Chi-restraints excluded: chain B residue 242 SER 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 148 THR Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 SER 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 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 187 HIS Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 131 LEU 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 51 VAL Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 68 PHE 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 45 SER 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 J residue 119 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain N residue 24 VAL 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: 0.5980 chunk 52 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 197 optimal weight: 0.0270 chunk 294 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN E 55 GLN E 191 GLN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN N 136 HIS ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.140107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.122311 restraints weight = 66456.938| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.71 r_work: 0.3862 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28498 Z= 0.192 Angle : 0.760 14.605 39044 Z= 0.392 Chirality : 0.046 0.319 4249 Planarity : 0.005 0.072 4666 Dihedral : 20.023 175.038 5142 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.74 % Favored : 89.84 % Rotamer: Outliers : 4.18 % Allowed : 28.63 % Favored : 67.19 % 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: -3.01 (0.14), residues: 3081 helix: -0.41 (0.15), residues: 1121 sheet: -2.82 (0.20), residues: 550 loop : -2.99 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 68 TYR 0.040 0.002 TYR M 175 PHE 0.039 0.002 PHE E 53 TRP 0.046 0.002 TRP H 146 HIS 0.008 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (28498) covalent geometry : angle 0.75959 / 0.39 (39044) hydrogen bonds : bond 0.06406 / 4.01 ( 878) hydrogen bonds : angle 5.42470 / 3.83 ( 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 628 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 517 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7215 (m-30) cc_final: 0.6924 (m-30) REVERT: A 16 GLN cc_start: 0.7373 (mm110) cc_final: 0.7044 (mt0) REVERT: A 145 HIS cc_start: 0.7712 (m90) cc_final: 0.7466 (m90) REVERT: A 150 MET cc_start: 0.6796 (ptp) cc_final: 0.6510 (ptp) REVERT: B 8 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: B 29 LEU cc_start: 0.8777 (pp) cc_final: 0.8566 (pp) REVERT: B 64 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5440 (m-30) REVERT: B 66 PHE cc_start: 0.3393 (OUTLIER) cc_final: 0.2685 (m-80) REVERT: B 90 GLU cc_start: 0.7073 (tp30) cc_final: 0.6637 (tm-30) REVERT: B 143 LEU cc_start: 0.8325 (mt) cc_final: 0.8030 (mt) REVERT: C 93 GLU cc_start: 0.7348 (pm20) cc_final: 0.6755 (tm-30) REVERT: C 103 CYS cc_start: 0.8025 (m) cc_final: 0.7260 (p) REVERT: C 270 ASP cc_start: 0.6304 (p0) cc_final: 0.5507 (p0) REVERT: D 25 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6371 (t0) REVERT: D 53 PHE cc_start: 0.5992 (t80) cc_final: 0.5647 (t80) REVERT: D 66 PHE cc_start: 0.4069 (t80) cc_final: 0.2738 (t80) REVERT: D 90 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6829 (tm-30) REVERT: D 106 TYR cc_start: 0.7284 (m-80) cc_final: 0.6974 (m-80) REVERT: D 116 MET cc_start: 0.7551 (mpp) cc_final: 0.7167 (mpp) REVERT: D 134 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.7942 (t) REVERT: D 141 MET cc_start: 0.7857 (mmt) cc_final: 0.7389 (mmt) REVERT: D 166 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7398 (p) REVERT: D 167 MET cc_start: 0.7840 (ttm) cc_final: 0.7480 (ttm) REVERT: D 220 GLN cc_start: 0.7541 (tt0) cc_final: 0.6890 (tt0) REVERT: D 221 MET cc_start: 0.7906 (mtm) cc_final: 0.7690 (mtp) REVERT: D 271 LYS cc_start: 0.8095 (pttm) cc_final: 0.7888 (pttm) REVERT: E 66 PHE cc_start: 0.5119 (OUTLIER) cc_final: 0.4121 (m-80) REVERT: E 94 LYS cc_start: 0.6852 (tttp) cc_final: 0.6148 (tmtt) REVERT: E 106 TYR cc_start: 0.7497 (m-80) cc_final: 0.6330 (t80) REVERT: E 156 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7734 (mmtt) REVERT: E 186 THR cc_start: 0.6976 (m) cc_final: 0.6605 (m) REVERT: E 271 LYS cc_start: 0.6340 (OUTLIER) cc_final: 0.5272 (mmtm) REVERT: F 167 MET cc_start: 0.5883 (ptp) cc_final: 0.5520 (ptt) REVERT: F 178 TYR cc_start: 0.6546 (m-80) cc_final: 0.6197 (m-80) REVERT: G 78 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7101 (tm-30) REVERT: G 107 HIS cc_start: 0.7427 (m-70) cc_final: 0.6951 (m-70) REVERT: H 1 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6470 (mpp) REVERT: H 29 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: H 59 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.6775 (mtm-85) REVERT: H 87 TYR cc_start: 0.6185 (m-80) cc_final: 0.5867 (m-80) REVERT: H 148 GLU cc_start: 0.7791 (tp30) cc_final: 0.7236 (tp30) REVERT: H 215 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8220 (m-40) REVERT: H 235 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6663 (tm-30) REVERT: H 271 THR cc_start: 0.8936 (m) cc_final: 0.8473 (p) REVERT: H 420 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8732 (mp) REVERT: H 579 PHE cc_start: 0.8238 (t80) cc_final: 0.8007 (t80) REVERT: I 65 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8594 (tppt) REVERT: I 67 GLU cc_start: 0.8998 (pt0) cc_final: 0.8642 (pt0) REVERT: I 87 GLN cc_start: 0.8426 (tp40) cc_final: 0.8025 (tp-100) REVERT: I 91 ASN cc_start: 0.8325 (m-40) cc_final: 0.8048 (m-40) REVERT: I 113 PHE cc_start: 0.8144 (m-80) cc_final: 0.7875 (m-80) REVERT: J 65 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8384 (mmmt) REVERT: M 53 PHE cc_start: 0.8262 (t80) cc_final: 0.7688 (t80) REVERT: M 116 MET cc_start: 0.8157 (mmt) cc_final: 0.7373 (tpt) REVERT: M 150 MET cc_start: 0.8463 (mtp) cc_final: 0.7915 (mtt) REVERT: M 178 TYR cc_start: 0.8932 (m-80) cc_final: 0.7855 (m-80) REVERT: M 186 THR cc_start: 0.6043 (OUTLIER) cc_final: 0.5818 (m) REVERT: M 280 ARG cc_start: 0.7506 (mmp-170) cc_final: 0.7284 (mmp-170) REVERT: N 25 SER cc_start: 0.8836 (p) cc_final: 0.8526 (m) REVERT: N 30 THR cc_start: 0.8773 (m) cc_final: 0.8364 (p) REVERT: N 36 ASN cc_start: 0.6243 (m-40) cc_final: 0.5837 (m-40) REVERT: N 69 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: N 89 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7000 (mm-40) REVERT: N 123 GLU cc_start: 0.8450 (tp30) cc_final: 0.7869 (tm-30) REVERT: N 125 PHE cc_start: 0.7945 (t80) cc_final: 0.7591 (t80) REVERT: N 136 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.5038 (t-170) REVERT: N 161 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.4775 (tt) REVERT: N 193 TYR cc_start: 0.8183 (t80) cc_final: 0.7887 (t80) outliers start: 111 outliers final: 83 residues processed: 585 average time/residue: 0.1855 time to fit residues: 175.5131 Evaluate side-chains 583 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 483 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 166 THR 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 242 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 212 HIS 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 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 187 HIS Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 175 TYR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 503 SER Chi-restraints excluded: chain H residue 552 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 SER 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 47 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 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 167 MET 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 260 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 89 GLN 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: 0.6980 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 139 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 300 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4256 r_free = 0.4256 target = 0.139911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.121780 restraints weight = 67180.079| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.77 r_work: 0.3855 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.7407 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= 0.185 Angle : 0.760 13.912 39044 Z= 0.393 Chirality : 0.046 0.241 4249 Planarity : 0.005 0.095 4666 Dihedral : 20.013 175.089 5142 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.52 % Favored : 89.06 % Rotamer: Outliers : 3.91 % Allowed : 29.23 % Favored : 66.85 % 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: -3.00 (0.14), residues: 3081 helix: -0.45 (0.15), residues: 1128 sheet: -2.79 (0.20), residues: 552 loop : -2.96 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 90 TYR 0.040 0.002 TYR M 175 PHE 0.043 0.002 PHE N 14 TRP 0.050 0.002 TRP H 146 HIS 0.013 0.001 HIS N 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (28498) covalent geometry : angle 0.75954 / 0.39 (39044) hydrogen bonds : bond 0.06299 / 3.97 ( 878) hydrogen bonds : angle 5.45299 / 3.85 ( 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 620 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 516 time to evaluate : 1.034 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: 0.7332 (m-30) cc_final: 0.7062 (m-30) REVERT: A 16 GLN cc_start: 0.7362 (mm110) cc_final: 0.7001 (mt0) REVERT: A 145 HIS cc_start: 0.7706 (m90) cc_final: 0.7435 (m90) REVERT: A 199 LEU cc_start: 0.7632 (tp) cc_final: 0.7428 (tp) REVERT: B 29 LEU cc_start: 0.8715 (pp) cc_final: 0.8506 (pp) REVERT: B 64 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5442 (m-30) REVERT: B 66 PHE cc_start: 0.3437 (OUTLIER) cc_final: 0.2770 (m-80) REVERT: B 90 GLU cc_start: 0.7003 (tp30) cc_final: 0.6554 (tm-30) REVERT: B 141 MET cc_start: 0.7503 (tpt) cc_final: 0.7192 (tpt) REVERT: B 143 LEU cc_start: 0.8403 (mt) cc_final: 0.8089 (mt) REVERT: B 247 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7340 (mm) REVERT: C 63 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7313 (m-70) REVERT: C 93 GLU cc_start: 0.7426 (pm20) cc_final: 0.6905 (tm-30) REVERT: C 103 CYS cc_start: 0.8068 (m) cc_final: 0.7288 (p) REVERT: C 270 ASP cc_start: 0.6547 (p0) cc_final: 0.5666 (p0) REVERT: D 25 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6370 (t0) REVERT: D 53 PHE cc_start: 0.6078 (t80) cc_final: 0.5734 (t80) REVERT: D 66 PHE cc_start: 0.4115 (t80) cc_final: 0.3076 (t80) REVERT: D 106 TYR cc_start: 0.7220 (m-80) cc_final: 0.7010 (m-80) REVERT: D 116 MET cc_start: 0.7575 (mpp) cc_final: 0.7157 (mpp) REVERT: D 134 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.7882 (t) REVERT: D 141 MET cc_start: 0.7770 (mmt) cc_final: 0.7290 (mmt) REVERT: D 167 MET cc_start: 0.7789 (ttm) cc_final: 0.7442 (ttm) REVERT: D 220 GLN cc_start: 0.7571 (tt0) cc_final: 0.6933 (tt0) REVERT: D 271 LYS cc_start: 0.8104 (pttm) cc_final: 0.7895 (pttm) REVERT: E 66 PHE cc_start: 0.4790 (OUTLIER) cc_final: 0.3665 (m-80) REVERT: E 94 LYS cc_start: 0.6915 (tttp) cc_final: 0.6259 (tmtt) REVERT: E 106 TYR cc_start: 0.7498 (m-80) cc_final: 0.6452 (t80) REVERT: E 156 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7714 (mmtt) REVERT: E 186 THR cc_start: 0.7199 (m) cc_final: 0.6415 (m) REVERT: E 204 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7476 (pp30) REVERT: E 241 ASP cc_start: 0.8060 (t70) cc_final: 0.7855 (t0) REVERT: E 271 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5310 (mmtm) REVERT: F 167 MET cc_start: 0.5800 (ptp) cc_final: 0.5416 (ptt) REVERT: F 178 TYR cc_start: 0.6535 (m-80) cc_final: 0.6169 (m-80) REVERT: G 74 GLN cc_start: 0.6392 (mp10) cc_final: 0.6136 (pm20) REVERT: G 77 TRP cc_start: 0.6509 (t60) cc_final: 0.6246 (t60) REVERT: G 78 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7194 (tm-30) REVERT: G 107 HIS cc_start: 0.7413 (m-70) cc_final: 0.6550 (m90) REVERT: H 1 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6769 (mpp) REVERT: H 29 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: H 59 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.6722 (mtp-110) REVERT: H 148 GLU cc_start: 0.7685 (tp30) cc_final: 0.7172 (tp30) REVERT: H 215 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8211 (m-40) REVERT: H 235 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6618 (tm-30) REVERT: H 236 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: H 271 THR cc_start: 0.8845 (m) cc_final: 0.8407 (p) REVERT: H 420 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8681 (mp) REVERT: H 579 PHE cc_start: 0.8238 (t80) cc_final: 0.7990 (t80) REVERT: I 65 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8482 (tppt) REVERT: I 67 GLU cc_start: 0.9017 (pt0) cc_final: 0.8637 (pt0) REVERT: I 87 GLN cc_start: 0.8451 (tp40) cc_final: 0.8066 (tp-100) REVERT: I 91 ASN cc_start: 0.8317 (m-40) cc_final: 0.8046 (m-40) REVERT: J 65 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8383 (mmmt) REVERT: J 74 GLN cc_start: 0.8234 (mp10) cc_final: 0.7940 (pm20) REVERT: M 53 PHE cc_start: 0.8254 (t80) cc_final: 0.7656 (t80) REVERT: M 116 MET cc_start: 0.8093 (mmt) cc_final: 0.7339 (tpp) REVERT: M 132 THR cc_start: 0.7514 (m) cc_final: 0.7291 (m) REVERT: M 150 MET cc_start: 0.8436 (mtp) cc_final: 0.7904 (mtt) REVERT: M 178 TYR cc_start: 0.8844 (m-80) cc_final: 0.7775 (m-80) REVERT: M 280 ARG cc_start: 0.7503 (mmp-170) cc_final: 0.7190 (mmp-170) REVERT: N 25 SER cc_start: 0.8708 (p) cc_final: 0.8490 (m) REVERT: N 36 ASN cc_start: 0.6219 (m-40) cc_final: 0.5924 (m-40) REVERT: N 69 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: N 89 GLN cc_start: 0.7931 (mt0) cc_final: 0.7453 (mm-40) REVERT: N 123 GLU cc_start: 0.8446 (tp30) cc_final: 0.7873 (tm-30) REVERT: N 125 PHE cc_start: 0.7946 (t80) cc_final: 0.7596 (t80) REVERT: N 161 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.4757 (tt) REVERT: N 193 TYR cc_start: 0.8070 (t80) cc_final: 0.7803 (t80) REVERT: N 202 ILE cc_start: 0.8549 (pt) cc_final: 0.8082 (tp) outliers start: 104 outliers final: 71 residues processed: 582 average time/residue: 0.1826 time to fit residues: 172.0020 Evaluate side-chains 570 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 483 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 265 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 212 HIS 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 77 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 17 ASP 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 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 175 TYR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 236 GLN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 66 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 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 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 GLU Chi-restraints excluded: chain N residue 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 296 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 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** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS E 191 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 542 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.135852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.117429 restraints weight = 67213.122| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.69 r_work: 0.3796 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.7825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 28498 Z= 0.230 Angle : 0.804 18.917 39044 Z= 0.414 Chirality : 0.047 0.300 4249 Planarity : 0.005 0.083 4666 Dihedral : 20.070 175.107 5142 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 26.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.10 % Favored : 88.48 % Rotamer: Outliers : 4.03 % Allowed : 29.68 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.64 (0.15), residues: 1136 sheet: -2.73 (0.20), residues: 570 loop : -2.96 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG J 80 TYR 0.034 0.002 TYR M 175 PHE 0.038 0.002 PHE G 122 TRP 0.054 0.002 TRP H 146 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (28498) covalent geometry : angle 0.80440 / 0.41 (39044) hydrogen bonds : bond 0.06369 / 4.02 ( 878) hydrogen bonds : angle 5.53090 / 3.91 ( 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 610 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 503 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7565 (mm110) cc_final: 0.7097 (mt0) REVERT: A 116 MET cc_start: 0.5287 (mtp) cc_final: 0.4738 (ttt) REVERT: A 145 HIS cc_start: 0.7803 (m90) cc_final: 0.7424 (m90) REVERT: B 33 ASP cc_start: 0.8032 (t0) cc_final: 0.7361 (t70) REVERT: B 64 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5641 (m-30) REVERT: B 66 PHE cc_start: 0.4011 (OUTLIER) cc_final: 0.3495 (m-80) REVERT: B 90 GLU cc_start: 0.7113 (tp30) cc_final: 0.6551 (tm-30) REVERT: B 143 LEU cc_start: 0.8524 (mt) cc_final: 0.8190 (mt) REVERT: C 6 ARG cc_start: 0.7124 (mmm-85) cc_final: 0.6408 (tpp80) REVERT: C 25 ASP cc_start: 0.7806 (m-30) cc_final: 0.7573 (m-30) REVERT: C 103 CYS cc_start: 0.8177 (m) cc_final: 0.7397 (p) REVERT: C 163 ASP cc_start: 0.7755 (t0) cc_final: 0.7522 (t0) REVERT: D 25 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6475 (t0) REVERT: D 116 MET cc_start: 0.7673 (mpp) cc_final: 0.7274 (mpp) REVERT: D 134 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.7904 (t) REVERT: D 141 MET cc_start: 0.7959 (mmt) cc_final: 0.7411 (mmt) REVERT: D 167 MET cc_start: 0.7954 (ttm) cc_final: 0.7624 (ttm) REVERT: D 220 GLN cc_start: 0.7652 (tt0) cc_final: 0.7114 (tt0) REVERT: E 66 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.3676 (m-80) REVERT: E 94 LYS cc_start: 0.7082 (tttp) cc_final: 0.6428 (tmtt) REVERT: E 156 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7573 (mmtt) REVERT: E 186 THR cc_start: 0.7735 (m) cc_final: 0.7522 (m) REVERT: E 271 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5595 (mmtm) REVERT: F 167 MET cc_start: 0.5801 (ptp) cc_final: 0.5434 (ptt) REVERT: F 178 TYR cc_start: 0.6641 (m-80) cc_final: 0.6248 (m-80) REVERT: F 248 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6541 (mm-40) REVERT: G 71 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8136 (mmm160) REVERT: G 78 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7287 (tm-30) REVERT: H 29 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: H 59 ARG cc_start: 0.7466 (mtp-110) cc_final: 0.6904 (mtp-110) REVERT: H 148 GLU cc_start: 0.7866 (tp30) cc_final: 0.7426 (tp30) REVERT: H 215 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8365 (m-40) REVERT: H 235 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6701 (tm-30) REVERT: H 236 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: H 271 THR cc_start: 0.8920 (m) cc_final: 0.8429 (p) REVERT: H 579 PHE cc_start: 0.8237 (t80) cc_final: 0.8011 (t80) REVERT: I 38 ASP cc_start: 0.8498 (m-30) cc_final: 0.8211 (t0) REVERT: I 65 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8491 (tppt) REVERT: I 87 GLN cc_start: 0.8407 (tp40) cc_final: 0.8069 (tp-100) REVERT: I 91 ASN cc_start: 0.8380 (m-40) cc_final: 0.8067 (m-40) REVERT: J 65 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8502 (mmmt) REVERT: M 132 THR cc_start: 0.7671 (m) cc_final: 0.7416 (m) REVERT: M 141 MET cc_start: 0.6863 (tpt) cc_final: 0.6109 (tpt) REVERT: M 150 MET cc_start: 0.8467 (mtp) cc_final: 0.7949 (mtt) REVERT: M 178 TYR cc_start: 0.9045 (m-80) cc_final: 0.7935 (m-80) REVERT: M 280 ARG cc_start: 0.7610 (mmp-170) cc_final: 0.7270 (mmp-170) REVERT: N 25 SER cc_start: 0.8833 (p) cc_final: 0.8468 (m) REVERT: N 30 THR cc_start: 0.8826 (m) cc_final: 0.8552 (p) REVERT: N 36 ASN cc_start: 0.6358 (m-40) cc_final: 0.5968 (m-40) REVERT: N 69 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: N 89 GLN cc_start: 0.7917 (mt0) cc_final: 0.7275 (mm-40) REVERT: N 123 GLU cc_start: 0.8544 (tp30) cc_final: 0.7978 (tm-30) REVERT: N 125 PHE cc_start: 0.8021 (t80) cc_final: 0.7694 (t80) REVERT: N 161 LEU cc_start: 0.5854 (OUTLIER) cc_final: 0.4853 (tt) REVERT: N 193 TYR cc_start: 0.8121 (t80) cc_final: 0.7840 (t80) REVERT: N 202 ILE cc_start: 0.8541 (pt) cc_final: 0.8110 (tp) outliers start: 107 outliers final: 78 residues processed: 569 average time/residue: 0.1880 time to fit residues: 171.3125 Evaluate side-chains 563 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 474 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 150 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 212 HIS 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 77 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 17 ASP 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 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 271 LYS 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 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 236 GLN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 24 ILE 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 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain 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 69 GLU 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: 0.8980 chunk 184 optimal weight: 0.0370 chunk 127 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 243 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 GLN H 417 GLN H 490 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 ASN ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.136673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.118305 restraints weight = 66643.780| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.72 r_work: 0.3804 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.7964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 28498 Z= 0.198 Angle : 0.807 16.234 39044 Z= 0.414 Chirality : 0.046 0.246 4249 Planarity : 0.005 0.091 4666 Dihedral : 20.071 174.534 5142 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.32 % Favored : 89.26 % Rotamer: Outliers : 3.46 % Allowed : 30.29 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.02 (0.14), residues: 3081 helix: -0.58 (0.15), residues: 1133 sheet: -2.73 (0.20), residues: 572 loop : -2.91 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 90 TYR 0.032 0.002 TYR N 26 PHE 0.057 0.002 PHE D 53 TRP 0.055 0.002 TRP H 146 HIS 0.010 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (28498) covalent geometry : angle 0.80718 / 0.41 (39044) hydrogen bonds : bond 0.06370 / 4.04 ( 878) hydrogen bonds : angle 5.52736 / 3.90 ( 2455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6518.68 seconds wall clock time: 113 minutes 18.88 seconds (6798.88 seconds total)