Starting phenix.real_space_refine on Mon Aug 25 10:14:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gan_29901/08_2025/8gan_29901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gan_29901/08_2025/8gan_29901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2025/8gan_29901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2025/8gan_29901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2025/8gan_29901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gan_29901/08_2025/8gan_29901.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 112 5.16 5 C 16933 2.51 5 N 4952 2.21 5 O 5536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 7.11, per 1000 atoms: 0.26 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: 2.60 Conformation dependent library (CDL) restraints added in 962.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5746 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 34 sheets defined 37.3% alpha, 11.0% beta 30 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 3.57 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: 4.47 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8646 1.34 - 1.46: 4875 1.46 - 1.57: 14520 1.57 - 1.69: 268 1.69 - 1.81: 189 Bond restraints: 28498 Sorted by residual: bond pdb=" C1' A K 15 " pdb=" N9 A K 15 " ideal model delta sigma weight residual 1.465 1.484 -0.019 1.50e-02 4.44e+03 1.69e+00 bond pdb=" C3' G K 30 " pdb=" O3' G K 30 " ideal model delta sigma weight residual 1.427 1.410 0.017 1.50e-02 4.44e+03 1.33e+00 bond pdb=" C1' G K 4 " pdb=" N9 G K 4 " ideal model delta sigma weight residual 1.465 1.480 -0.015 1.50e-02 4.44e+03 1.05e+00 bond pdb=" C3' C K 21 " pdb=" O3' C K 21 " ideal model delta sigma weight residual 1.427 1.412 0.015 1.50e-02 4.44e+03 1.02e+00 bond pdb=" C3' U K 42 " pdb=" O3' U K 42 " ideal model delta sigma weight residual 1.427 1.412 0.015 1.50e-02 4.44e+03 9.91e-01 ... (remaining 28493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 38398 1.51 - 3.03: 550 3.03 - 4.54: 72 4.54 - 6.06: 22 6.06 - 7.57: 2 Bond angle restraints: 39044 Sorted by residual: angle pdb=" C3' G K 4 " pdb=" O3' G K 4 " pdb=" P A K 5 " ideal model delta sigma weight residual 120.20 125.66 -5.46 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P G K 10 " ideal model delta sigma weight residual 120.20 125.08 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" C ARG C 68 " pdb=" N GLU C 69 " pdb=" CA GLU C 69 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" O3' G K 4 " pdb=" C3' G K 4 " pdb=" C2' G K 4 " ideal model delta sigma weight residual 109.50 113.69 -4.19 1.50e+00 4.44e-01 7.81e+00 angle pdb=" C GLU D 90 " pdb=" N LYS D 91 " pdb=" CA LYS D 91 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.80e+00 ... (remaining 39039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 15886 35.87 - 71.74: 1032 71.74 - 107.60: 51 107.60 - 143.47: 3 143.47 - 179.34: 3 Dihedral angle restraints: 16975 sinusoidal: 8036 harmonic: 8939 Sorted by residual: dihedral pdb=" C4' C K 22 " pdb=" C3' C K 22 " pdb=" C2' C K 22 " pdb=" C1' C K 22 " ideal model delta sinusoidal sigma weight residual -35.00 31.00 -66.00 1 8.00e+00 1.56e-02 8.90e+01 dihedral pdb=" C5' C K 22 " pdb=" C4' C K 22 " pdb=" C3' C K 22 " pdb=" O3' C K 22 " ideal model delta sinusoidal sigma weight residual 147.00 83.58 63.42 1 8.00e+00 1.56e-02 8.29e+01 dihedral pdb=" O4' C K 22 " pdb=" C4' C K 22 " pdb=" C3' C K 22 " pdb=" C2' C K 22 " ideal model delta sinusoidal sigma weight residual 24.00 -32.67 56.67 1 8.00e+00 1.56e-02 6.76e+01 ... (remaining 16972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3639 0.050 - 0.100: 530 0.100 - 0.151: 74 0.151 - 0.201: 2 0.201 - 0.251: 4 Chirality restraints: 4249 Sorted by residual: chirality pdb=" C3' C K 22 " pdb=" C4' C K 22 " pdb=" O3' C K 22 " pdb=" C2' C K 22 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C2' C K 22 " pdb=" C3' C K 22 " pdb=" O2' C K 22 " pdb=" C1' C K 22 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4246 not shown) Planarity restraints: 4666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A K 6 " 0.031 2.00e-02 2.50e+03 1.38e-02 5.20e+00 pdb=" N9 A K 6 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A K 6 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A K 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A K 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A K 6 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A K 6 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A K 6 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A K 6 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A K 6 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C K 31 " 0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 C K 31 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C K 31 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C K 31 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C K 31 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C K 31 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C K 31 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C K 31 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C K 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 514 " -0.164 9.50e-02 1.11e+02 7.36e-02 3.43e+00 pdb=" NE ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG H 514 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 514 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 514 " -0.008 2.00e-02 2.50e+03 ... (remaining 4663 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 516 2.63 - 3.20: 23692 3.20 - 3.76: 47482 3.76 - 4.33: 65574 4.33 - 4.90: 104393 Nonbonded interactions: 241657 Sorted by model distance: nonbonded pdb=" N2 G K 30 " pdb=" O2 DC L 25 " model vdw 2.060 2.496 nonbonded pdb=" O THR A 148 " pdb=" O2' C K 31 " model vdw 2.135 3.040 nonbonded pdb=" O THR B 148 " pdb=" O2' U K 19 " model vdw 2.144 3.040 nonbonded pdb=" N2 G K 27 " pdb=" O2 DC L 28 " model vdw 2.161 2.496 nonbonded pdb=" O2 C K 43 " pdb=" N2 DG L 12 " model vdw 2.179 2.496 ... (remaining 241652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.150 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28498 Z= 0.106 Angle : 0.448 7.574 39044 Z= 0.247 Chirality : 0.036 0.251 4249 Planarity : 0.003 0.074 4666 Dihedral : 20.282 179.338 11229 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 2.89 % Allowed : 13.63 % Favored : 83.48 % Rotamer: Outliers : 3.05 % Allowed : 20.50 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00204 (28498) covalent geometry : angle 0.44770 (39044) hydrogen bonds : bond 0.18318 ( 878) hydrogen bonds : angle 6.41266 ( 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 : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.2211 (OUTLIER) cc_final: 0.1998 (m-80) REVERT: A 147 ILE cc_start: 0.6579 (pt) cc_final: 0.6377 (pt) REVERT: C 66 PHE cc_start: 0.2217 (OUTLIER) cc_final: 0.1562 (m-80) REVERT: C 150 MET cc_start: 0.5846 (ptm) cc_final: 0.5400 (ptm) REVERT: D 53 PHE cc_start: 0.1101 (t80) cc_final: 0.0764 (t80) REVERT: D 153 THR cc_start: 0.3888 (OUTLIER) cc_final: 0.3656 (m) REVERT: E 273 LEU cc_start: 0.3861 (pp) cc_final: 0.3339 (tp) REVERT: F 66 PHE cc_start: 0.3434 (OUTLIER) cc_final: 0.1847 (t80) REVERT: F 214 HIS cc_start: 0.4919 (m-70) cc_final: 0.4654 (m-70) REVERT: G 21 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7742 (mt) REVERT: H 48 THR cc_start: 0.6527 (p) cc_final: 0.6289 (p) REVERT: H 73 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6718 (mtmm) REVERT: H 141 MET cc_start: 0.7798 (mpp) cc_final: 0.7449 (mmm) REVERT: H 155 CYS cc_start: 0.4920 (t) cc_final: 0.4202 (t) REVERT: H 505 PRO cc_start: 0.6413 (Cg_exo) cc_final: 0.6067 (Cg_endo) REVERT: H 549 HIS cc_start: 0.6908 (t-90) cc_final: 0.6589 (t-90) REVERT: N 36 ASN cc_start: 0.2953 (m-40) cc_final: 0.2447 (m110) REVERT: N 83 ILE cc_start: 0.6968 (pt) cc_final: 0.6509 (pt) outliers start: 81 outliers final: 10 residues processed: 1072 average time/residue: 0.1946 time to fit residues: 318.3692 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 : 0.976 ------------------------------------------------------------------------------- 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: 4.9990 chunk 248 optimal weight: 4.9990 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: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS A 234 ASN B 145 HIS B 181 HIS ** 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 145 HIS D 181 HIS D 204 GLN D 220 GLN D 231 HIS E 62 HIS E 83 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 231 HIS ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS G 98 GLN 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 ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN M 55 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN 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 = 0.4580 r_free = 0.4580 target = 0.166024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.149066 restraints weight = 69767.786| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 4.28 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28498 Z= 0.200 Angle : 0.775 15.791 39044 Z= 0.396 Chirality : 0.046 0.230 4249 Planarity : 0.005 0.056 4666 Dihedral : 19.712 176.585 5160 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.68 % Favored : 88.87 % Rotamer: Outliers : 4.55 % Allowed : 23.89 % Favored : 71.56 % 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 aren not related in a simple way. whole: -3.25 (0.14), residues: 3081 helix: -0.41 (0.15), residues: 1112 sheet: -2.96 (0.21), residues: 455 loop : -3.35 (0.13), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 143 TYR 0.033 0.002 TYR J 40 PHE 0.034 0.002 PHE G 52 TRP 0.028 0.002 TRP J 77 HIS 0.009 0.002 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00431 (28498) covalent geometry : angle 0.77517 (39044) hydrogen bonds : bond 0.06307 ( 878) hydrogen bonds : angle 5.24314 ( 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 782 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 661 time to evaluate : 1.050 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: A 16 GLN cc_start: 0.7282 (mp10) cc_final: 0.6835 (mm-40) REVERT: A 63 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.7040 (t-90) REVERT: A 124 GLN cc_start: 0.3928 (mm-40) cc_final: 0.2858 (mt0) REVERT: A 150 MET cc_start: 0.6047 (ptp) cc_final: 0.5812 (ptp) REVERT: B 7 TYR cc_start: 0.6796 (m-80) cc_final: 0.6080 (m-80) REVERT: B 145 HIS cc_start: 0.7619 (m-70) cc_final: 0.7051 (m170) REVERT: B 165 ARG cc_start: 0.7568 (mtt-85) cc_final: 0.7243 (mtt-85) REVERT: B 196 GLU cc_start: 0.7575 (tp30) cc_final: 0.6596 (tm-30) REVERT: B 204 GLN cc_start: 0.7652 (pt0) cc_final: 0.7431 (pp30) REVERT: C 56 MET cc_start: 0.3941 (ptt) cc_final: 0.3194 (mtt) REVERT: C 64 ASP cc_start: 0.4045 (OUTLIER) cc_final: 0.3522 (m-30) REVERT: C 93 GLU cc_start: 0.7165 (pm20) cc_final: 0.6499 (tm-30) REVERT: C 157 ASP cc_start: 0.7583 (m-30) cc_final: 0.7262 (m-30) REVERT: D 4 GLU cc_start: 0.6767 (pp20) cc_final: 0.6447 (pp20) REVERT: D 25 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6501 (t0) REVERT: D 62 HIS cc_start: 0.8242 (t-90) cc_final: 0.7986 (t70) REVERT: D 93 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7628 (mm-30) REVERT: D 150 MET cc_start: 0.6586 (ptp) cc_final: 0.6369 (ptp) REVERT: D 167 MET cc_start: 0.7008 (ttm) cc_final: 0.6528 (ttm) REVERT: E 4 GLU cc_start: 0.7538 (pm20) cc_final: 0.7129 (pm20) REVERT: E 66 PHE cc_start: 0.3178 (OUTLIER) cc_final: 0.2387 (m-10) REVERT: E 204 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8165 (pp30) REVERT: E 212 HIS cc_start: 0.4513 (m170) cc_final: 0.3460 (m-70) REVERT: E 272 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6851 (t0) REVERT: E 273 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.3724 (tp) REVERT: F 56 MET cc_start: 0.6592 (ptp) cc_final: 0.6255 (ptp) REVERT: H 29 GLU cc_start: 0.8161 (tt0) cc_final: 0.7351 (tp30) REVERT: H 33 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8646 (tp) REVERT: H 48 THR cc_start: 0.7600 (p) cc_final: 0.7135 (p) REVERT: H 102 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8390 (mtmm) REVERT: H 149 CYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6425 (p) REVERT: H 420 LEU cc_start: 0.8713 (mp) cc_final: 0.8444 (mp) REVERT: H 453 MET cc_start: 0.8180 (mtp) cc_final: 0.7914 (mtp) REVERT: I 45 SER cc_start: 0.3998 (t) cc_final: 0.3609 (t) REVERT: I 56 MET cc_start: 0.8815 (mmt) cc_final: 0.8511 (mmm) REVERT: I 88 ARG cc_start: 0.8095 (ttt-90) cc_final: 0.7688 (ttt-90) REVERT: I 91 ASN cc_start: 0.7156 (m-40) cc_final: 0.6631 (m-40) REVERT: I 96 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7594 (mt-10) REVERT: I 98 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7822 (tp40) REVERT: I 119 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7831 (mtmm) REVERT: J 46 SER cc_start: 0.6867 (p) cc_final: 0.6528 (m) REVERT: J 88 ARG cc_start: 0.8529 (tmt170) cc_final: 0.8304 (ttt90) REVERT: J 89 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.6278 (m-10) REVERT: M 53 PHE cc_start: 0.7621 (t80) cc_final: 0.7077 (t80) REVERT: M 64 ASP cc_start: 0.8018 (m-30) cc_final: 0.7541 (m-30) REVERT: M 178 TYR cc_start: 0.8480 (m-80) cc_final: 0.7664 (m-80) REVERT: M 269 ASP cc_start: 0.7302 (t0) cc_final: 0.7066 (t0) REVERT: M 279 LEU cc_start: 0.7887 (tt) cc_final: 0.7663 (tt) REVERT: N 36 ASN cc_start: 0.5099 (m-40) cc_final: 0.4560 (m110) REVERT: N 64 ASN cc_start: 0.7033 (p0) cc_final: 0.6600 (p0) REVERT: N 126 LYS cc_start: 0.8951 (tppt) cc_final: 0.8634 (tppt) REVERT: N 161 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.3531 (tt) outliers start: 121 outliers final: 45 residues processed: 726 average time/residue: 0.1947 time to fit residues: 222.9297 Evaluate side-chains 574 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 516 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 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 103 CYS 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 172 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 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 264 TYR Chi-restraints excluded: chain G residue 17 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 102 LYS Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain N residue 3 PHE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 306 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 8 optimal weight: 0.0040 chunk 277 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 318 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 55 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN B 35 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 197 ASN C 220 GLN E 231 HIS E 233 ASN F 130 GLN ** 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 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN M 231 HIS ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.159832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.142868 restraints weight = 68334.492| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 4.00 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28498 Z= 0.174 Angle : 0.717 14.103 39044 Z= 0.366 Chirality : 0.044 0.218 4249 Planarity : 0.004 0.050 4666 Dihedral : 19.600 176.686 5145 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.65 % Favored : 88.96 % Rotamer: Outliers : 4.67 % Allowed : 23.59 % Favored : 71.75 % 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 aren not related in a simple way. whole: -3.04 (0.14), residues: 3081 helix: -0.15 (0.15), residues: 1115 sheet: -2.85 (0.21), residues: 461 loop : -3.31 (0.13), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 101 TYR 0.024 0.002 TYR E 7 PHE 0.029 0.002 PHE E 183 TRP 0.032 0.002 TRP H 146 HIS 0.012 0.002 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00394 (28498) covalent geometry : angle 0.71671 (39044) hydrogen bonds : bond 0.05880 ( 878) hydrogen bonds : angle 5.13936 ( 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 697 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 573 time to evaluate : 1.088 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: A 16 GLN cc_start: 0.7243 (mp10) cc_final: 0.6460 (mm-40) REVERT: A 21 ASN cc_start: 0.7485 (t0) cc_final: 0.7140 (t0) REVERT: A 56 MET cc_start: 0.4430 (mtp) cc_final: 0.4030 (mtt) REVERT: A 63 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6817 (t-90) REVERT: A 64 ASP cc_start: 0.6217 (OUTLIER) cc_final: 0.5462 (m-30) REVERT: B 7 TYR cc_start: 0.7235 (m-80) cc_final: 0.6877 (m-80) REVERT: B 211 ASP cc_start: 0.5870 (m-30) cc_final: 0.5609 (m-30) REVERT: B 264 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.4809 (m-80) REVERT: C 93 GLU cc_start: 0.7112 (pm20) cc_final: 0.6487 (tm-30) REVERT: C 103 CYS cc_start: 0.6057 (p) cc_final: 0.5549 (p) REVERT: D 4 GLU cc_start: 0.6968 (pp20) cc_final: 0.6718 (pp20) REVERT: D 11 PHE cc_start: 0.6012 (t80) cc_final: 0.5742 (t80) REVERT: D 25 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6089 (t0) REVERT: D 93 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7755 (mm-30) REVERT: D 141 MET cc_start: 0.7672 (mmt) cc_final: 0.7466 (mmt) REVERT: D 145 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7329 (m-70) REVERT: D 166 THR cc_start: 0.6227 (OUTLIER) cc_final: 0.5951 (p) REVERT: D 167 MET cc_start: 0.7056 (ttm) cc_final: 0.6647 (ttm) REVERT: D 221 MET cc_start: 0.7099 (mtm) cc_final: 0.6533 (mtp) REVERT: E 66 PHE cc_start: 0.3363 (OUTLIER) cc_final: 0.2353 (m-10) REVERT: E 163 ASP cc_start: 0.3052 (OUTLIER) cc_final: 0.2755 (p0) REVERT: E 204 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8271 (pp30) REVERT: E 235 LEU cc_start: 0.4154 (OUTLIER) cc_final: 0.3953 (tt) REVERT: E 271 LYS cc_start: 0.5120 (OUTLIER) cc_final: 0.4783 (pptt) REVERT: E 273 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.3946 (tp) REVERT: F 53 PHE cc_start: 0.7502 (t80) cc_final: 0.7050 (t80) REVERT: F 56 MET cc_start: 0.6349 (ptp) cc_final: 0.6116 (ptp) REVERT: F 66 PHE cc_start: 0.3034 (OUTLIER) cc_final: 0.1820 (t80) REVERT: F 204 GLN cc_start: 0.8897 (pt0) cc_final: 0.8610 (pp30) REVERT: G 56 MET cc_start: 0.8008 (mmt) cc_final: 0.7676 (mmt) REVERT: G 77 TRP cc_start: 0.6570 (t60) cc_final: 0.6160 (t60) REVERT: H 141 MET cc_start: 0.8939 (mpp) cc_final: 0.8710 (mmt) REVERT: H 146 TRP cc_start: 0.7844 (t60) cc_final: 0.7571 (t60) REVERT: H 215 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8214 (m-40) REVERT: H 235 GLU cc_start: 0.5962 (tm-30) cc_final: 0.5542 (tm-30) REVERT: H 326 TYR cc_start: 0.8190 (m-80) cc_final: 0.7922 (m-10) REVERT: H 563 TYR cc_start: 0.8311 (t80) cc_final: 0.8001 (t80) REVERT: I 88 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7788 (ttt-90) REVERT: I 91 ASN cc_start: 0.7314 (m-40) cc_final: 0.6971 (m-40) REVERT: I 119 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7689 (mtmm) REVERT: J 77 TRP cc_start: 0.7066 (t60) cc_final: 0.6862 (t60) REVERT: J 107 HIS cc_start: 0.6919 (m-70) cc_final: 0.6455 (m-70) REVERT: M 53 PHE cc_start: 0.7898 (t80) cc_final: 0.7526 (t80) REVERT: M 102 MET cc_start: 0.8070 (ttm) cc_final: 0.7808 (ttp) REVERT: M 178 TYR cc_start: 0.8528 (m-80) cc_final: 0.7806 (m-80) REVERT: N 36 ASN cc_start: 0.5062 (m-40) cc_final: 0.4441 (m110) REVERT: N 64 ASN cc_start: 0.6895 (p0) cc_final: 0.6680 (p0) REVERT: N 94 LEU cc_start: 0.8815 (mt) cc_final: 0.8603 (mt) REVERT: N 161 LEU cc_start: 0.4752 (OUTLIER) cc_final: 0.3768 (tt) REVERT: N 193 TYR cc_start: 0.7673 (t80) cc_final: 0.7296 (t80) outliers start: 124 outliers final: 62 residues processed: 650 average time/residue: 0.1960 time to fit residues: 202.4163 Evaluate side-chains 564 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 487 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 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 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 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 54 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 148 THR 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 67 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE 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 140 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 LYS 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 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 33 ILE Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 80 ARG 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 108 ASP Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 3 PHE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 154 LYS 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: 6.9990 chunk 129 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 58 GLN E 62 HIS F 21 ASN F 35 GLN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN H 4 HIS H 41 ASN H 156 ASN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 GLN H 531 GLN H 542 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 ASN M 212 HIS ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN N 187 ASN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.129095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109538 restraints weight = 66428.342| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.84 r_work: 0.3639 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 28498 Z= 0.398 Angle : 1.003 17.647 39044 Z= 0.512 Chirality : 0.054 0.269 4249 Planarity : 0.007 0.077 4666 Dihedral : 20.198 179.040 5143 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 33.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.98 % Favored : 87.60 % Rotamer: Outliers : 6.58 % Allowed : 23.36 % Favored : 70.05 % 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 aren not related in a simple way. whole: -3.26 (0.14), residues: 3081 helix: -0.58 (0.15), residues: 1132 sheet: -3.10 (0.19), residues: 507 loop : -3.15 (0.14), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 259 TYR 0.030 0.003 TYR E 178 PHE 0.049 0.004 PHE E 183 TRP 0.032 0.003 TRP J 77 HIS 0.024 0.003 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00844 (28498) covalent geometry : angle 1.00268 (39044) hydrogen bonds : bond 0.07611 ( 878) hydrogen bonds : angle 5.92310 ( 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 787 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 612 time to evaluate : 1.032 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 17 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6732 (m-30) REVERT: A 56 MET cc_start: 0.6339 (mtp) cc_final: 0.5966 (mtt) REVERT: A 72 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.6584 (mm) REVERT: A 144 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 150 MET cc_start: 0.8188 (ptp) cc_final: 0.7743 (ptp) REVERT: B 33 ASP cc_start: 0.8671 (t0) cc_final: 0.7940 (t70) REVERT: B 66 PHE cc_start: 0.3941 (OUTLIER) cc_final: 0.3065 (m-10) REVERT: B 72 ILE cc_start: 0.6367 (mp) cc_final: 0.5961 (mp) REVERT: B 90 GLU cc_start: 0.7796 (tp30) cc_final: 0.7066 (tm-30) REVERT: B 116 MET cc_start: 0.7669 (mpp) cc_final: 0.7118 (mpp) REVERT: C 8 ASP cc_start: 0.8618 (m-30) cc_final: 0.8159 (m-30) REVERT: C 23 ASP cc_start: 0.7829 (t0) cc_final: 0.7556 (t0) REVERT: C 43 ASP cc_start: 0.8236 (p0) cc_final: 0.8000 (p0) REVERT: C 93 GLU cc_start: 0.7602 (pm20) cc_final: 0.6739 (tm-30) REVERT: C 100 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7459 (mm-40) REVERT: C 163 ASP cc_start: 0.8743 (t0) cc_final: 0.7107 (t0) REVERT: C 166 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8213 (p) REVERT: C 245 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8609 (mmtm) REVERT: C 248 GLN cc_start: 0.8415 (mm110) cc_final: 0.8005 (mp10) REVERT: C 258 VAL cc_start: 0.6323 (p) cc_final: 0.5300 (m) REVERT: D 25 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6656 (t0) REVERT: D 72 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6810 (tp) REVERT: D 141 MET cc_start: 0.7791 (mmt) cc_final: 0.7387 (mmt) REVERT: D 160 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8319 (tm-30) REVERT: D 161 THR cc_start: 0.8510 (p) cc_final: 0.8130 (p) REVERT: D 220 GLN cc_start: 0.8144 (tt0) cc_final: 0.7771 (tt0) REVERT: D 221 MET cc_start: 0.8265 (mtm) cc_final: 0.7853 (mtp) REVERT: E 53 PHE cc_start: 0.6876 (t80) cc_final: 0.6449 (t80) REVERT: E 56 MET cc_start: 0.8595 (mtt) cc_final: 0.7962 (mtm) REVERT: E 66 PHE cc_start: 0.4702 (OUTLIER) cc_final: 0.3771 (m-10) REVERT: E 94 LYS cc_start: 0.7060 (tttp) cc_final: 0.6063 (tmtt) REVERT: E 184 ILE cc_start: 0.9120 (mt) cc_final: 0.8836 (mm) REVERT: E 186 THR cc_start: 0.8033 (m) cc_final: 0.7686 (m) REVERT: E 206 LEU cc_start: 0.8991 (tp) cc_final: 0.8558 (tp) REVERT: E 230 GLU cc_start: 0.5703 (mp0) cc_final: 0.5313 (mp0) REVERT: E 235 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6632 (tp) REVERT: F 49 LYS cc_start: 0.8346 (mttp) cc_final: 0.8064 (ttmt) REVERT: F 53 PHE cc_start: 0.8042 (t80) cc_final: 0.7665 (t80) REVERT: F 66 PHE cc_start: 0.4465 (OUTLIER) cc_final: 0.3130 (t80) REVERT: F 100 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8413 (mm110) REVERT: F 167 MET cc_start: 0.5940 (ptp) cc_final: 0.5717 (ptp) REVERT: F 204 GLN cc_start: 0.8916 (pt0) cc_final: 0.8500 (tm-30) REVERT: G 56 MET cc_start: 0.8355 (mmt) cc_final: 0.8119 (mmt) REVERT: G 77 TRP cc_start: 0.6900 (t60) cc_final: 0.6650 (t60) REVERT: G 103 ILE cc_start: 0.7912 (mm) cc_final: 0.6315 (mm) REVERT: G 107 HIS cc_start: 0.7974 (m-70) cc_final: 0.6745 (m90) REVERT: H 26 GLU cc_start: 0.7872 (pt0) cc_final: 0.7653 (pt0) REVERT: H 29 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: H 47 ASP cc_start: 0.8121 (p0) cc_final: 0.7651 (p0) REVERT: H 87 TYR cc_start: 0.7308 (m-80) cc_final: 0.7065 (m-80) REVERT: H 98 GLU cc_start: 0.8629 (tp30) cc_final: 0.8326 (pt0) REVERT: H 102 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8607 (mtmm) REVERT: H 215 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8326 (m-40) REVERT: H 235 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7191 (tm-30) REVERT: H 289 ILE cc_start: 0.7360 (mm) cc_final: 0.7033 (mm) REVERT: H 324 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8334 (mmmt) REVERT: H 327 LEU cc_start: 0.8741 (tt) cc_final: 0.8499 (tp) REVERT: H 342 TRP cc_start: 0.8484 (t-100) cc_final: 0.8125 (t-100) REVERT: H 344 GLU cc_start: 0.8404 (tt0) cc_final: 0.8076 (pm20) REVERT: H 346 THR cc_start: 0.8221 (p) cc_final: 0.8006 (t) REVERT: I 12 TYR cc_start: 0.8087 (t80) cc_final: 0.7857 (t80) REVERT: I 67 GLU cc_start: 0.8979 (pt0) cc_final: 0.8628 (tm-30) REVERT: I 87 GLN cc_start: 0.8065 (pm20) cc_final: 0.7568 (tp-100) REVERT: I 91 ASN cc_start: 0.8281 (m-40) cc_final: 0.7932 (m-40) REVERT: I 97 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8866 (mm-40) REVERT: J 74 GLN cc_start: 0.8588 (mt0) cc_final: 0.7965 (mm-40) REVERT: J 77 TRP cc_start: 0.7774 (t60) cc_final: 0.7324 (t60) REVERT: J 120 ASN cc_start: 0.8318 (m-40) cc_final: 0.7419 (m-40) REVERT: M 53 PHE cc_start: 0.8440 (t80) cc_final: 0.7815 (t80) REVERT: M 65 ILE cc_start: 0.8191 (mm) cc_final: 0.7901 (mm) REVERT: M 134 SER cc_start: 0.9447 (m) cc_final: 0.8671 (p) REVERT: M 150 MET cc_start: 0.8740 (mtp) cc_final: 0.7579 (mtt) REVERT: M 178 TYR cc_start: 0.9250 (m-80) cc_final: 0.7929 (m-80) REVERT: M 279 LEU cc_start: 0.8140 (tt) cc_final: 0.7810 (tt) REVERT: N 26 TYR cc_start: 0.8709 (m-80) cc_final: 0.7945 (m-80) REVERT: N 68 ASN cc_start: 0.7262 (m110) cc_final: 0.6575 (m110) REVERT: N 69 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: N 97 ASP cc_start: 0.8318 (m-30) cc_final: 0.7935 (t0) REVERT: N 117 ASN cc_start: 0.8397 (t0) cc_final: 0.8162 (m110) REVERT: N 124 MET cc_start: 0.8940 (ptp) cc_final: 0.8580 (ptp) REVERT: N 136 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.4765 (t70) REVERT: N 147 CYS cc_start: 0.7017 (m) cc_final: 0.6664 (m) REVERT: N 161 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5450 (mp) REVERT: N 175 MET cc_start: 0.7125 (mpp) cc_final: 0.6200 (mtt) REVERT: N 179 LYS cc_start: 0.7324 (pttp) cc_final: 0.7023 (pttp) REVERT: N 186 ASN cc_start: 0.8266 (p0) cc_final: 0.7643 (p0) REVERT: N 187 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6910 (p0) outliers start: 175 outliers final: 88 residues processed: 717 average time/residue: 0.2028 time to fit residues: 228.1131 Evaluate side-chains 594 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 489 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 172 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 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP 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 129 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 129 VAL 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 232 SER 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 66 PHE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 17 LEU 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 102 LYS Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 539 ILE 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 I residue 100 LEU Chi-restraints excluded: chain J residue 17 LEU 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 42 THR Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 209 MET Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 57 LEU 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 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 187 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 15 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 259 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 145 HIS ** 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 220 GLN E 208 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN M 63 HIS ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.132140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.113919 restraints weight = 65815.654| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.69 r_work: 0.3731 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.8029 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= 0.195 Angle : 0.773 16.569 39044 Z= 0.391 Chirality : 0.045 0.344 4249 Planarity : 0.005 0.059 4666 Dihedral : 19.954 173.080 5143 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.32 % Favored : 89.29 % Rotamer: Outliers : 4.40 % Allowed : 26.37 % Favored : 69.22 % 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 aren not related in a simple way. whole: -3.05 (0.14), residues: 3081 helix: -0.37 (0.15), residues: 1137 sheet: -3.06 (0.19), residues: 543 loop : -3.02 (0.14), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 68 TYR 0.018 0.002 TYR N 100 PHE 0.030 0.002 PHE D 53 TRP 0.032 0.002 TRP H 146 HIS 0.011 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00446 (28498) covalent geometry : angle 0.77268 (39044) hydrogen bonds : bond 0.06150 ( 878) hydrogen bonds : angle 5.54288 ( 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 670 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 553 time to evaluate : 1.055 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 68 ARG cc_start: 0.6235 (ttt180) cc_final: 0.5985 (tpt-90) REVERT: A 144 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 150 MET cc_start: 0.7972 (ptp) cc_final: 0.7646 (ptp) REVERT: A 199 LEU cc_start: 0.7886 (tp) cc_final: 0.7575 (tp) REVERT: A 212 HIS cc_start: 0.6381 (m90) cc_final: 0.5962 (m90) REVERT: A 248 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7221 (mp10) REVERT: B 66 PHE cc_start: 0.4856 (OUTLIER) cc_final: 0.4132 (m-80) REVERT: B 90 GLU cc_start: 0.7643 (tp30) cc_final: 0.6948 (tm-30) REVERT: B 116 MET cc_start: 0.7501 (mpp) cc_final: 0.6817 (mpp) REVERT: B 196 GLU cc_start: 0.8289 (tp30) cc_final: 0.7840 (tm-30) REVERT: B 211 ASP cc_start: 0.7505 (m-30) cc_final: 0.7024 (m-30) REVERT: C 8 ASP cc_start: 0.8700 (m-30) cc_final: 0.8199 (m-30) REVERT: C 23 ASP cc_start: 0.7916 (t0) cc_final: 0.7617 (t0) REVERT: C 93 GLU cc_start: 0.7548 (pm20) cc_final: 0.6717 (tm-30) REVERT: C 103 CYS cc_start: 0.7506 (p) cc_final: 0.7178 (t) REVERT: C 107 TYR cc_start: 0.8411 (t80) cc_final: 0.7724 (t80) REVERT: C 111 THR cc_start: 0.7916 (p) cc_final: 0.7595 (p) REVERT: C 166 THR cc_start: 0.8170 (t) cc_final: 0.7961 (p) REVERT: D 23 ASP cc_start: 0.8173 (t0) cc_final: 0.7886 (t0) REVERT: D 66 PHE cc_start: 0.3788 (t80) cc_final: 0.2707 (t80) REVERT: D 106 TYR cc_start: 0.6939 (m-80) cc_final: 0.6027 (m-80) REVERT: D 116 MET cc_start: 0.7792 (mpp) cc_final: 0.7271 (mpp) REVERT: D 141 MET cc_start: 0.7865 (mmt) cc_final: 0.7358 (mmt) REVERT: D 160 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8236 (tm-30) REVERT: D 167 MET cc_start: 0.8037 (ttm) cc_final: 0.7478 (ttm) REVERT: D 220 GLN cc_start: 0.8029 (tt0) cc_final: 0.7706 (tt0) REVERT: D 221 MET cc_start: 0.8181 (mtm) cc_final: 0.7958 (mtp) REVERT: E 56 MET cc_start: 0.8536 (mtt) cc_final: 0.7961 (mtm) REVERT: E 66 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.4086 (m-10) REVERT: E 94 LYS cc_start: 0.6989 (tttp) cc_final: 0.6358 (tmtt) REVERT: E 106 TYR cc_start: 0.7356 (m-80) cc_final: 0.6071 (t80) REVERT: E 186 THR cc_start: 0.7856 (m) cc_final: 0.7514 (m) REVERT: E 230 GLU cc_start: 0.5737 (mp0) cc_final: 0.5324 (mp0) REVERT: E 241 ASP cc_start: 0.8288 (t70) cc_final: 0.8001 (t0) REVERT: F 49 LYS cc_start: 0.8185 (mttp) cc_final: 0.7956 (ttmt) REVERT: F 53 PHE cc_start: 0.8025 (t80) cc_final: 0.7632 (t80) REVERT: F 100 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8323 (mm110) REVERT: F 167 MET cc_start: 0.6157 (ptp) cc_final: 0.5804 (ptt) REVERT: F 187 HIS cc_start: 0.6897 (t-170) cc_final: 0.6545 (t-170) REVERT: F 204 GLN cc_start: 0.8838 (pt0) cc_final: 0.8510 (tm-30) REVERT: F 248 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6706 (mm-40) REVERT: G 62 HIS cc_start: 0.8700 (m170) cc_final: 0.8429 (m-70) REVERT: G 68 PHE cc_start: 0.5541 (m-80) cc_final: 0.4915 (m-80) REVERT: G 77 TRP cc_start: 0.6973 (t60) cc_final: 0.6617 (t60) REVERT: G 107 HIS cc_start: 0.7734 (m-70) cc_final: 0.6555 (m90) REVERT: G 108 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8573 (tm-30) REVERT: H 26 GLU cc_start: 0.7946 (pt0) cc_final: 0.7684 (pt0) REVERT: H 85 TYR cc_start: 0.8039 (p90) cc_final: 0.7635 (p90) REVERT: H 102 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8647 (mtmm) REVERT: H 141 MET cc_start: 0.8959 (mpp) cc_final: 0.8605 (mpp) REVERT: H 148 GLU cc_start: 0.7739 (tp30) cc_final: 0.7326 (tp30) REVERT: H 171 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: H 195 CYS cc_start: 0.7606 (m) cc_final: 0.7259 (m) REVERT: H 215 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8116 (m-40) REVERT: H 235 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6855 (tm-30) REVERT: H 327 LEU cc_start: 0.8685 (tt) cc_final: 0.8414 (tp) REVERT: H 342 TRP cc_start: 0.8473 (t-100) cc_final: 0.8008 (t-100) REVERT: H 344 GLU cc_start: 0.8270 (tt0) cc_final: 0.7811 (pm20) REVERT: H 579 PHE cc_start: 0.8261 (t80) cc_final: 0.7841 (t80) REVERT: I 57 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8150 (mtm-85) REVERT: I 87 GLN cc_start: 0.7847 (pm20) cc_final: 0.7403 (tp-100) REVERT: I 91 ASN cc_start: 0.8205 (m-40) cc_final: 0.7834 (m-40) REVERT: I 108 GLU cc_start: 0.8235 (tp30) cc_final: 0.7235 (tp30) REVERT: J 65 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8836 (mmmt) REVERT: J 74 GLN cc_start: 0.8611 (mt0) cc_final: 0.8076 (mp10) REVERT: M 43 ASP cc_start: 0.8250 (p0) cc_final: 0.7996 (p0) REVERT: M 53 PHE cc_start: 0.8239 (t80) cc_final: 0.7579 (t80) REVERT: M 72 ILE cc_start: 0.7286 (tt) cc_final: 0.7021 (tt) REVERT: M 102 MET cc_start: 0.8782 (ttm) cc_final: 0.8251 (ttp) REVERT: M 134 SER cc_start: 0.9366 (m) cc_final: 0.8595 (p) REVERT: M 150 MET cc_start: 0.8507 (mtp) cc_final: 0.7639 (mtt) REVERT: M 167 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8540 (mpp) REVERT: M 178 TYR cc_start: 0.9219 (m-80) cc_final: 0.8181 (m-80) REVERT: M 280 ARG cc_start: 0.7345 (mmp-170) cc_final: 0.7092 (mmp-170) REVERT: N 19 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8348 (mp) REVERT: N 26 TYR cc_start: 0.8500 (m-80) cc_final: 0.8267 (m-80) REVERT: N 69 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: N 97 ASP cc_start: 0.8190 (m-30) cc_final: 0.7780 (t0) REVERT: N 124 MET cc_start: 0.8868 (ptp) cc_final: 0.8524 (ptp) REVERT: N 147 CYS cc_start: 0.6662 (m) cc_final: 0.6012 (m) REVERT: N 161 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.4874 (tt) outliers start: 117 outliers final: 66 residues processed: 629 average time/residue: 0.1930 time to fit residues: 193.5673 Evaluate side-chains 562 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 487 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 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 116 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 62 HIS Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 167 MET Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 209 MET Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 19 LEU 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 154 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 220 optimal weight: 0.0770 chunk 153 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 81 HIS ** A 83 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN E 55 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN H 531 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN J 91 ASN J 120 ASN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.131775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.113412 restraints weight = 65832.763| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.76 r_work: 0.3716 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.8257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28498 Z= 0.195 Angle : 0.752 15.294 39044 Z= 0.381 Chirality : 0.045 0.363 4249 Planarity : 0.005 0.061 4666 Dihedral : 19.883 170.404 5143 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.42 % Favored : 89.19 % Rotamer: Outliers : 4.14 % Allowed : 26.90 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.14), residues: 3081 helix: -0.35 (0.15), residues: 1132 sheet: -2.96 (0.19), residues: 567 loop : -2.91 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 66 TYR 0.034 0.002 TYR M 175 PHE 0.038 0.002 PHE E 53 TRP 0.042 0.002 TRP H 146 HIS 0.009 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00439 (28498) covalent geometry : angle 0.75158 (39044) hydrogen bonds : bond 0.05907 ( 878) hydrogen bonds : angle 5.44718 ( 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 639 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 529 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7751 (mp10) cc_final: 0.7334 (mp10) REVERT: A 116 MET cc_start: 0.6462 (mtp) cc_final: 0.6195 (ttt) REVERT: A 199 LEU cc_start: 0.7938 (tp) cc_final: 0.7628 (tp) REVERT: B 4 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 90 GLU cc_start: 0.7656 (tp30) cc_final: 0.7020 (tm-30) REVERT: B 141 MET cc_start: 0.7506 (tpp) cc_final: 0.6687 (tpp) REVERT: B 143 LEU cc_start: 0.8619 (mt) cc_final: 0.8382 (mt) REVERT: B 196 GLU cc_start: 0.8359 (tp30) cc_final: 0.7794 (tm-30) REVERT: B 211 ASP cc_start: 0.7520 (m-30) cc_final: 0.7094 (m-30) REVERT: C 8 ASP cc_start: 0.8693 (m-30) cc_final: 0.8245 (m-30) REVERT: C 10 VAL cc_start: 0.8630 (t) cc_final: 0.8082 (m) REVERT: C 23 ASP cc_start: 0.7818 (t0) cc_final: 0.7508 (t0) REVERT: C 93 GLU cc_start: 0.7606 (pm20) cc_final: 0.6919 (tm-30) REVERT: C 107 TYR cc_start: 0.8437 (t80) cc_final: 0.7807 (t80) REVERT: C 111 THR cc_start: 0.8061 (p) cc_final: 0.7655 (p) REVERT: C 178 TYR cc_start: 0.8106 (m-10) cc_final: 0.7563 (m-10) REVERT: C 209 MET cc_start: 0.8271 (ptt) cc_final: 0.7930 (ttp) REVERT: C 221 MET cc_start: 0.8662 (ttp) cc_final: 0.8256 (ttt) REVERT: D 23 ASP cc_start: 0.7940 (t0) cc_final: 0.7615 (t0) REVERT: D 25 ASP cc_start: 0.6846 (t0) cc_final: 0.6559 (t0) REVERT: D 67 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5506 (mp) REVERT: D 106 TYR cc_start: 0.6933 (m-80) cc_final: 0.6018 (m-80) REVERT: D 141 MET cc_start: 0.7864 (mmt) cc_final: 0.7447 (mmt) REVERT: D 161 THR cc_start: 0.8173 (p) cc_final: 0.7744 (p) REVERT: D 220 GLN cc_start: 0.8056 (tt0) cc_final: 0.7783 (tt0) REVERT: D 221 MET cc_start: 0.8273 (mtm) cc_final: 0.8045 (mtp) REVERT: E 53 PHE cc_start: 0.7519 (t80) cc_final: 0.7247 (t80) REVERT: E 56 MET cc_start: 0.8424 (mtt) cc_final: 0.7940 (mtt) REVERT: E 66 PHE cc_start: 0.4578 (OUTLIER) cc_final: 0.3812 (m-10) REVERT: E 76 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6840 (tt) REVERT: E 94 LYS cc_start: 0.7124 (tttp) cc_final: 0.6588 (tmtt) REVERT: E 116 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5593 (ppp) REVERT: E 186 THR cc_start: 0.8069 (m) cc_final: 0.6887 (m) REVERT: E 230 GLU cc_start: 0.5957 (mp0) cc_final: 0.5491 (mp0) REVERT: E 241 ASP cc_start: 0.8377 (t70) cc_final: 0.8155 (t0) REVERT: F 49 LYS cc_start: 0.8234 (mttp) cc_final: 0.8026 (ttmm) REVERT: F 53 PHE cc_start: 0.8048 (t80) cc_final: 0.7498 (t80) REVERT: F 100 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8192 (mm110) REVERT: F 167 MET cc_start: 0.6150 (ptp) cc_final: 0.5788 (ptt) REVERT: F 187 HIS cc_start: 0.6808 (t-170) cc_final: 0.6465 (t-170) REVERT: F 204 GLN cc_start: 0.8840 (pt0) cc_final: 0.8596 (tm-30) REVERT: G 68 PHE cc_start: 0.5506 (m-80) cc_final: 0.4851 (m-80) REVERT: G 74 GLN cc_start: 0.6489 (mp10) cc_final: 0.6276 (mp10) REVERT: G 83 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7435 (tt) REVERT: G 106 TYR cc_start: 0.8437 (m-80) cc_final: 0.8192 (m-80) REVERT: G 107 HIS cc_start: 0.7772 (m-70) cc_final: 0.6431 (m90) REVERT: G 108 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8313 (tm-30) REVERT: H 26 GLU cc_start: 0.7953 (pt0) cc_final: 0.7672 (pt0) REVERT: H 59 ARG cc_start: 0.7616 (mtp-110) cc_final: 0.6894 (mtp-110) REVERT: H 85 TYR cc_start: 0.7893 (p90) cc_final: 0.7479 (p90) REVERT: H 102 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8582 (mtmm) REVERT: H 148 GLU cc_start: 0.7797 (tp30) cc_final: 0.7512 (tp30) REVERT: H 171 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: H 195 CYS cc_start: 0.7583 (m) cc_final: 0.7254 (m) REVERT: H 215 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8171 (m-40) REVERT: H 235 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6939 (tm-30) REVERT: H 289 ILE cc_start: 0.7589 (mm) cc_final: 0.7330 (mm) REVERT: H 327 LEU cc_start: 0.8651 (tt) cc_final: 0.8383 (tp) REVERT: H 342 TRP cc_start: 0.8499 (t-100) cc_final: 0.8070 (t-100) REVERT: H 344 GLU cc_start: 0.8283 (tt0) cc_final: 0.7773 (pm20) REVERT: H 579 PHE cc_start: 0.8175 (t80) cc_final: 0.7803 (t80) REVERT: I 65 LYS cc_start: 0.9132 (tppp) cc_final: 0.8805 (ttmm) REVERT: I 68 PHE cc_start: 0.8574 (m-80) cc_final: 0.8311 (m-80) REVERT: I 87 GLN cc_start: 0.7939 (pm20) cc_final: 0.7471 (tp-100) REVERT: I 91 ASN cc_start: 0.8112 (m-40) cc_final: 0.7739 (m-40) REVERT: I 98 GLN cc_start: 0.8607 (tp40) cc_final: 0.8250 (tp-100) REVERT: I 108 GLU cc_start: 0.8223 (tp30) cc_final: 0.7791 (tp30) REVERT: J 51 VAL cc_start: 0.8579 (m) cc_final: 0.8292 (p) REVERT: J 65 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8800 (mmmt) REVERT: J 74 GLN cc_start: 0.8604 (mt0) cc_final: 0.8128 (mp10) REVERT: M 43 ASP cc_start: 0.8221 (p0) cc_final: 0.7974 (p0) REVERT: M 53 PHE cc_start: 0.8180 (t80) cc_final: 0.7427 (t80) REVERT: M 102 MET cc_start: 0.8797 (ttm) cc_final: 0.8264 (ttp) REVERT: M 132 THR cc_start: 0.7499 (m) cc_final: 0.7239 (m) REVERT: M 150 MET cc_start: 0.8383 (mtp) cc_final: 0.7514 (mtt) REVERT: M 167 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8486 (mpp) REVERT: M 178 TYR cc_start: 0.9128 (m-80) cc_final: 0.7810 (m-80) REVERT: M 247 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7997 (mt) REVERT: N 19 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8356 (mp) REVERT: N 68 ASN cc_start: 0.7725 (m-40) cc_final: 0.7508 (m-40) REVERT: N 69 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: N 97 ASP cc_start: 0.8140 (m-30) cc_final: 0.7738 (t0) REVERT: N 124 MET cc_start: 0.8894 (ptp) cc_final: 0.8508 (ptp) REVERT: N 147 CYS cc_start: 0.6075 (m) cc_final: 0.5735 (m) REVERT: N 161 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5352 (mt) REVERT: N 175 MET cc_start: 0.6779 (mpp) cc_final: 0.6450 (mtm) outliers start: 110 outliers final: 70 residues processed: 597 average time/residue: 0.1829 time to fit residues: 175.4266 Evaluate side-chains 572 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 488 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 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 116 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 116 MET 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 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 167 MET Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 64 ASN Chi-restraints excluded: chain N residue 65 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 198 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 58 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 220 GLN D 52 ASN E 55 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN F 63 HIS F 130 GLN G 98 GLN H 236 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 HIS N 61 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.131502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.112934 restraints weight = 66083.321| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.78 r_work: 0.3717 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.8442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28498 Z= 0.181 Angle : 0.737 14.914 39044 Z= 0.374 Chirality : 0.044 0.184 4249 Planarity : 0.005 0.083 4666 Dihedral : 19.860 171.252 5143 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.03 % Favored : 89.55 % Rotamer: Outliers : 4.03 % Allowed : 27.80 % Favored : 68.17 % 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 aren not related in a simple way. whole: -2.91 (0.14), residues: 3081 helix: -0.29 (0.15), residues: 1109 sheet: -2.90 (0.18), residues: 588 loop : -2.86 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 90 TYR 0.026 0.002 TYR M 175 PHE 0.051 0.002 PHE N 14 TRP 0.047 0.002 TRP H 146 HIS 0.009 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00417 (28498) covalent geometry : angle 0.73748 (39044) hydrogen bonds : bond 0.05760 ( 878) hydrogen bonds : angle 5.35028 ( 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 618 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 511 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7807 (mp10) cc_final: 0.7331 (mp10) REVERT: A 199 LEU cc_start: 0.8138 (tp) cc_final: 0.7879 (tp) REVERT: B 4 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 35 GLN cc_start: 0.8242 (mp10) cc_final: 0.8036 (mp10) REVERT: B 66 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.3940 (m-80) REVERT: B 90 GLU cc_start: 0.7683 (tp30) cc_final: 0.7051 (tm-30) REVERT: B 143 LEU cc_start: 0.8610 (mt) cc_final: 0.7948 (mt) REVERT: B 196 GLU cc_start: 0.8383 (tp30) cc_final: 0.7797 (tm-30) REVERT: B 211 ASP cc_start: 0.7691 (m-30) cc_final: 0.7285 (m-30) REVERT: C 8 ASP cc_start: 0.8642 (m-30) cc_final: 0.8220 (m-30) REVERT: C 23 ASP cc_start: 0.7674 (t0) cc_final: 0.7223 (t0) REVERT: D 23 ASP cc_start: 0.8051 (t0) cc_final: 0.7765 (t0) REVERT: D 25 ASP cc_start: 0.6778 (t0) cc_final: 0.6486 (t0) REVERT: D 67 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5486 (mp) REVERT: D 106 TYR cc_start: 0.6796 (m-80) cc_final: 0.6122 (m-80) REVERT: D 141 MET cc_start: 0.7769 (mmt) cc_final: 0.7473 (mmt) REVERT: D 167 MET cc_start: 0.8341 (ttm) cc_final: 0.7927 (ttm) REVERT: D 220 GLN cc_start: 0.8075 (tt0) cc_final: 0.7764 (tt0) REVERT: D 221 MET cc_start: 0.8324 (mtm) cc_final: 0.8099 (mtp) REVERT: E 56 MET cc_start: 0.8415 (mtt) cc_final: 0.8138 (mtp) REVERT: E 66 PHE cc_start: 0.4654 (OUTLIER) cc_final: 0.3870 (m-10) REVERT: E 94 LYS cc_start: 0.7193 (tttp) cc_final: 0.6716 (tttp) REVERT: E 106 TYR cc_start: 0.7244 (m-80) cc_final: 0.5928 (t80) REVERT: E 116 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5614 (ppp) REVERT: E 186 THR cc_start: 0.7928 (m) cc_final: 0.7689 (m) REVERT: E 207 VAL cc_start: 0.8626 (t) cc_final: 0.8291 (m) REVERT: E 208 ASN cc_start: 0.8245 (m110) cc_final: 0.7795 (m-40) REVERT: E 211 ASP cc_start: 0.8467 (m-30) cc_final: 0.7936 (t70) REVERT: E 230 GLU cc_start: 0.6072 (mp0) cc_final: 0.5315 (mp0) REVERT: E 241 ASP cc_start: 0.8368 (t70) cc_final: 0.8096 (t0) REVERT: F 49 LYS cc_start: 0.8305 (mttp) cc_final: 0.8075 (ttmt) REVERT: F 53 PHE cc_start: 0.8070 (t80) cc_final: 0.7510 (t80) REVERT: F 100 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8215 (mm110) REVERT: F 167 MET cc_start: 0.6115 (ptp) cc_final: 0.5752 (ptt) REVERT: F 187 HIS cc_start: 0.6939 (t-170) cc_final: 0.6702 (t-170) REVERT: F 204 GLN cc_start: 0.8894 (pt0) cc_final: 0.8627 (tm-30) REVERT: F 248 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6596 (mm-40) REVERT: G 5 ARG cc_start: 0.7337 (mtp85) cc_final: 0.6998 (mtt-85) REVERT: G 68 PHE cc_start: 0.5566 (m-80) cc_final: 0.4859 (m-80) REVERT: G 83 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7721 (tp) REVERT: G 107 HIS cc_start: 0.7735 (m-70) cc_final: 0.6396 (m90) REVERT: G 108 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8260 (tm-30) REVERT: H 26 GLU cc_start: 0.7981 (pt0) cc_final: 0.7694 (pt0) REVERT: H 59 ARG cc_start: 0.7611 (mtp-110) cc_final: 0.6853 (mtp-110) REVERT: H 148 GLU cc_start: 0.7921 (tp30) cc_final: 0.7702 (tp30) REVERT: H 171 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: H 195 CYS cc_start: 0.7678 (m) cc_final: 0.7418 (m) REVERT: H 215 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: H 235 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6961 (tm-30) REVERT: H 251 THR cc_start: 0.8586 (p) cc_final: 0.8384 (p) REVERT: H 289 ILE cc_start: 0.7671 (mm) cc_final: 0.7431 (mm) REVERT: H 327 LEU cc_start: 0.8602 (tt) cc_final: 0.8387 (tp) REVERT: H 342 TRP cc_start: 0.8495 (t-100) cc_final: 0.8131 (t-100) REVERT: H 344 GLU cc_start: 0.8267 (tt0) cc_final: 0.7910 (pm20) REVERT: H 579 PHE cc_start: 0.8128 (t80) cc_final: 0.7776 (t80) REVERT: I 65 LYS cc_start: 0.9089 (tppp) cc_final: 0.8815 (ttmm) REVERT: I 68 PHE cc_start: 0.8536 (m-80) cc_final: 0.8198 (m-80) REVERT: I 76 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7687 (mm-40) REVERT: I 87 GLN cc_start: 0.8566 (pm20) cc_final: 0.8016 (tp-100) REVERT: I 91 ASN cc_start: 0.8139 (m-40) cc_final: 0.7797 (m-40) REVERT: I 98 GLN cc_start: 0.8559 (tp40) cc_final: 0.8205 (tp-100) REVERT: J 65 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8597 (mmmt) REVERT: J 74 GLN cc_start: 0.8520 (mt0) cc_final: 0.7995 (mp10) REVERT: M 53 PHE cc_start: 0.8113 (t80) cc_final: 0.7419 (t80) REVERT: M 132 THR cc_start: 0.7505 (m) cc_final: 0.7203 (m) REVERT: M 150 MET cc_start: 0.8335 (mtp) cc_final: 0.7711 (mtp) REVERT: M 167 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8310 (mpp) REVERT: M 178 TYR cc_start: 0.9087 (m-80) cc_final: 0.7715 (m-80) REVERT: M 247 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7942 (mt) REVERT: N 19 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8326 (mp) REVERT: N 69 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: N 97 ASP cc_start: 0.8101 (m-30) cc_final: 0.7569 (t0) REVERT: N 123 GLU cc_start: 0.8868 (tp30) cc_final: 0.8180 (tm-30) REVERT: N 147 CYS cc_start: 0.5984 (m) cc_final: 0.5766 (m) REVERT: N 161 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5085 (tt) outliers start: 107 outliers final: 67 residues processed: 581 average time/residue: 0.1603 time to fit residues: 149.1393 Evaluate side-chains 556 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 476 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 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 116 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 60 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 116 MET 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 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 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 N residue 19 LEU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 64 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 chunk 249 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 294 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN 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 124 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 HIS J 91 ASN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.128248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.110059 restraints weight = 65872.753| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.63 r_work: 0.3677 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.8774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28498 Z= 0.206 Angle : 0.760 15.266 39044 Z= 0.384 Chirality : 0.044 0.171 4249 Planarity : 0.005 0.115 4666 Dihedral : 19.865 170.739 5141 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.78 % Favored : 88.80 % Rotamer: Outliers : 4.03 % Allowed : 28.14 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.14), residues: 3081 helix: -0.25 (0.15), residues: 1111 sheet: -2.83 (0.19), residues: 602 loop : -2.85 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 90 TYR 0.024 0.002 TYR M 175 PHE 0.051 0.002 PHE N 14 TRP 0.052 0.002 TRP H 146 HIS 0.013 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00472 (28498) covalent geometry : angle 0.75964 (39044) hydrogen bonds : bond 0.05772 ( 878) hydrogen bonds : angle 5.37865 ( 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 605 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 498 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7710 (mp10) cc_final: 0.7456 (mp-120) REVERT: A 56 MET cc_start: 0.7004 (mmm) cc_final: 0.6136 (mmm) REVERT: A 199 LEU cc_start: 0.8105 (tp) cc_final: 0.7846 (tp) REVERT: A 245 LYS cc_start: 0.8645 (mttt) cc_final: 0.8233 (mmtt) REVERT: B 4 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 66 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4341 (m-80) REVERT: B 90 GLU cc_start: 0.7685 (tp30) cc_final: 0.7013 (tm-30) REVERT: B 141 MET cc_start: 0.7724 (tpp) cc_final: 0.7372 (tpp) REVERT: B 253 ASP cc_start: 0.7427 (p0) cc_final: 0.7128 (p0) REVERT: C 8 ASP cc_start: 0.8666 (m-30) cc_final: 0.8335 (m-30) REVERT: C 23 ASP cc_start: 0.7626 (t0) cc_final: 0.7306 (t0) REVERT: C 166 THR cc_start: 0.8166 (t) cc_final: 0.7878 (p) REVERT: C 209 MET cc_start: 0.8383 (ptt) cc_final: 0.8023 (ttp) REVERT: D 4 GLU cc_start: 0.7683 (pp20) cc_final: 0.7077 (pp20) REVERT: D 8 ASP cc_start: 0.8293 (t70) cc_final: 0.8046 (m-30) REVERT: D 23 ASP cc_start: 0.7913 (t0) cc_final: 0.7648 (t0) REVERT: D 67 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5915 (mp) REVERT: D 106 TYR cc_start: 0.6816 (m-80) cc_final: 0.6274 (m-80) REVERT: D 141 MET cc_start: 0.7757 (mmt) cc_final: 0.7317 (mmt) REVERT: D 143 LEU cc_start: 0.8790 (mt) cc_final: 0.8559 (mt) REVERT: D 167 MET cc_start: 0.8243 (ttm) cc_final: 0.7771 (ttm) REVERT: D 220 GLN cc_start: 0.8066 (tt0) cc_final: 0.7798 (tt0) REVERT: E 56 MET cc_start: 0.8506 (mtt) cc_final: 0.8169 (mtp) REVERT: E 66 PHE cc_start: 0.4751 (OUTLIER) cc_final: 0.3979 (m-10) REVERT: E 94 LYS cc_start: 0.7374 (tttp) cc_final: 0.6942 (tttp) REVERT: E 116 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5541 (ppp) REVERT: E 207 VAL cc_start: 0.8660 (t) cc_final: 0.8458 (m) REVERT: E 208 ASN cc_start: 0.7797 (m110) cc_final: 0.7266 (m-40) REVERT: E 230 GLU cc_start: 0.5775 (mp0) cc_final: 0.4780 (mp0) REVERT: E 241 ASP cc_start: 0.8516 (t70) cc_final: 0.8213 (t0) REVERT: F 53 PHE cc_start: 0.8059 (t80) cc_final: 0.7499 (t80) REVERT: F 100 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8121 (mm110) REVERT: F 167 MET cc_start: 0.6005 (ptp) cc_final: 0.5609 (ptt) REVERT: F 187 HIS cc_start: 0.7124 (t-170) cc_final: 0.6597 (t-170) REVERT: F 204 GLN cc_start: 0.8887 (pt0) cc_final: 0.8533 (tm-30) REVERT: F 248 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6626 (mm-40) REVERT: G 5 ARG cc_start: 0.7352 (mtp85) cc_final: 0.7043 (mtt-85) REVERT: G 68 PHE cc_start: 0.5793 (m-80) cc_final: 0.5132 (m-80) REVERT: G 107 HIS cc_start: 0.7782 (m-70) cc_final: 0.6400 (m90) REVERT: G 108 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8248 (tm-30) REVERT: H 26 GLU cc_start: 0.7942 (pt0) cc_final: 0.7582 (pt0) REVERT: H 59 ARG cc_start: 0.7621 (mtp-110) cc_final: 0.6905 (mtp-110) REVERT: H 148 GLU cc_start: 0.7911 (tp30) cc_final: 0.7697 (tp30) REVERT: H 171 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: H 195 CYS cc_start: 0.7778 (m) cc_final: 0.7541 (m) REVERT: H 215 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8262 (m-40) REVERT: H 235 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6853 (tm-30) REVERT: H 251 THR cc_start: 0.8612 (p) cc_final: 0.8393 (p) REVERT: H 289 ILE cc_start: 0.7725 (mm) cc_final: 0.7426 (mt) REVERT: H 327 LEU cc_start: 0.8621 (tt) cc_final: 0.8420 (tp) REVERT: H 342 TRP cc_start: 0.8522 (t-100) cc_final: 0.8209 (t-100) REVERT: H 344 GLU cc_start: 0.8372 (tt0) cc_final: 0.7972 (pm20) REVERT: H 393 LEU cc_start: 0.8394 (mp) cc_final: 0.8113 (mp) REVERT: H 446 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7775 (ttp-110) REVERT: H 579 PHE cc_start: 0.8099 (t80) cc_final: 0.7826 (t80) REVERT: I 65 LYS cc_start: 0.9100 (tppp) cc_final: 0.8853 (ttmm) REVERT: I 68 PHE cc_start: 0.8490 (m-80) cc_final: 0.8112 (m-80) REVERT: I 76 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7917 (mm-40) REVERT: I 87 GLN cc_start: 0.8570 (pm20) cc_final: 0.8011 (tp-100) REVERT: I 91 ASN cc_start: 0.8192 (m-40) cc_final: 0.7871 (m-40) REVERT: J 65 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8623 (mmmt) REVERT: J 74 GLN cc_start: 0.8636 (mt0) cc_final: 0.8086 (mp10) REVERT: M 53 PHE cc_start: 0.8209 (t80) cc_final: 0.7454 (t80) REVERT: M 102 MET cc_start: 0.8771 (ttm) cc_final: 0.8488 (ttm) REVERT: M 150 MET cc_start: 0.8011 (mtp) cc_final: 0.7480 (mtp) REVERT: M 167 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8275 (mpp) REVERT: M 175 TYR cc_start: 0.8627 (t80) cc_final: 0.8235 (t80) REVERT: M 178 TYR cc_start: 0.9088 (m-80) cc_final: 0.7597 (m-80) REVERT: M 247 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7941 (mt) REVERT: N 19 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8342 (mp) REVERT: N 69 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: N 97 ASP cc_start: 0.8095 (m-30) cc_final: 0.7640 (t0) REVERT: N 123 GLU cc_start: 0.8891 (tp30) cc_final: 0.8221 (tm-30) REVERT: N 147 CYS cc_start: 0.6405 (m) cc_final: 0.5955 (m) REVERT: N 161 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5158 (tt) REVERT: N 175 MET cc_start: 0.6907 (mtm) cc_final: 0.6316 (mtt) outliers start: 107 outliers final: 75 residues processed: 564 average time/residue: 0.1609 time to fit residues: 146.3675 Evaluate side-chains 552 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 465 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 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 33 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain E residue 60 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 116 MET 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 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 167 MET Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 64 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 136 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.127565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108995 restraints weight = 66346.875| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.69 r_work: 0.3655 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.9024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28498 Z= 0.202 Angle : 0.771 16.476 39044 Z= 0.388 Chirality : 0.044 0.189 4249 Planarity : 0.005 0.069 4666 Dihedral : 19.882 171.264 5141 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.58 % Favored : 89.00 % Rotamer: Outliers : 3.46 % Allowed : 28.74 % Favored : 67.80 % 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 aren not related in a simple way. whole: -2.83 (0.14), residues: 3081 helix: -0.29 (0.15), residues: 1108 sheet: -2.75 (0.19), residues: 596 loop : -2.81 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 66 TYR 0.025 0.002 TYR H 312 PHE 0.049 0.002 PHE A 53 TRP 0.056 0.002 TRP H 146 HIS 0.010 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00464 (28498) covalent geometry : angle 0.77060 (39044) hydrogen bonds : bond 0.05756 ( 878) hydrogen bonds : angle 5.38181 ( 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 580 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 488 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7803 (mp10) cc_final: 0.7579 (mp10) REVERT: A 150 MET cc_start: 0.8117 (ptp) cc_final: 0.7490 (ptp) REVERT: A 245 LYS cc_start: 0.8559 (mttt) cc_final: 0.8150 (mmtt) REVERT: B 4 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: B 66 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.4697 (m-80) REVERT: B 90 GLU cc_start: 0.7700 (tp30) cc_final: 0.7020 (tm-30) REVERT: B 141 MET cc_start: 0.7683 (tpp) cc_final: 0.7106 (tpp) REVERT: B 196 GLU cc_start: 0.8469 (tp30) cc_final: 0.7974 (tm-30) REVERT: C 8 ASP cc_start: 0.8615 (m-30) cc_final: 0.8144 (m-30) REVERT: C 23 ASP cc_start: 0.7550 (t0) cc_final: 0.7222 (t0) REVERT: C 25 ASP cc_start: 0.8024 (m-30) cc_final: 0.7461 (m-30) REVERT: C 107 TYR cc_start: 0.8500 (t80) cc_final: 0.7758 (t80) REVERT: C 166 THR cc_start: 0.8108 (t) cc_final: 0.7819 (p) REVERT: C 209 MET cc_start: 0.8414 (ptt) cc_final: 0.7848 (ttp) REVERT: D 4 GLU cc_start: 0.7817 (pp20) cc_final: 0.7221 (pp20) REVERT: D 8 ASP cc_start: 0.8407 (t70) cc_final: 0.8206 (m-30) REVERT: D 23 ASP cc_start: 0.7721 (t0) cc_final: 0.7501 (t0) REVERT: D 67 ILE cc_start: 0.6006 (OUTLIER) cc_final: 0.5694 (mp) REVERT: D 106 TYR cc_start: 0.6844 (m-80) cc_final: 0.6265 (m-80) REVERT: D 141 MET cc_start: 0.7733 (mmt) cc_final: 0.7261 (mmt) REVERT: D 143 LEU cc_start: 0.8928 (mt) cc_final: 0.8427 (mt) REVERT: D 167 MET cc_start: 0.8044 (ttm) cc_final: 0.7719 (ttm) REVERT: D 220 GLN cc_start: 0.8080 (tt0) cc_final: 0.7846 (tt0) REVERT: E 56 MET cc_start: 0.8464 (mtt) cc_final: 0.8149 (mtt) REVERT: E 94 LYS cc_start: 0.7526 (tttp) cc_final: 0.7242 (tttp) REVERT: E 116 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5113 (ppp) REVERT: E 208 ASN cc_start: 0.7810 (m110) cc_final: 0.7542 (m-40) REVERT: E 241 ASP cc_start: 0.8416 (t70) cc_final: 0.8104 (t0) REVERT: E 264 TYR cc_start: 0.2035 (OUTLIER) cc_final: 0.1734 (m-10) REVERT: F 53 PHE cc_start: 0.7968 (t80) cc_final: 0.7588 (t80) REVERT: F 100 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8028 (mm110) REVERT: F 167 MET cc_start: 0.6011 (ptp) cc_final: 0.5607 (ptt) REVERT: F 187 HIS cc_start: 0.7463 (t-170) cc_final: 0.6995 (t-170) REVERT: F 204 GLN cc_start: 0.8883 (pt0) cc_final: 0.8533 (tm-30) REVERT: F 248 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6815 (mm-40) REVERT: G 5 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6942 (mtt-85) REVERT: G 68 PHE cc_start: 0.5770 (m-80) cc_final: 0.5112 (m-80) REVERT: G 107 HIS cc_start: 0.7755 (m-70) cc_final: 0.6306 (m90) REVERT: G 108 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8026 (tm-30) REVERT: H 26 GLU cc_start: 0.7926 (pt0) cc_final: 0.7552 (pt0) REVERT: H 59 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.6774 (mtp-110) REVERT: H 171 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: H 195 CYS cc_start: 0.7811 (m) cc_final: 0.7411 (m) REVERT: H 215 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8271 (m-40) REVERT: H 235 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6762 (tm-30) REVERT: H 251 THR cc_start: 0.8620 (p) cc_final: 0.8403 (p) REVERT: H 289 ILE cc_start: 0.7663 (mm) cc_final: 0.7391 (mt) REVERT: H 342 TRP cc_start: 0.8573 (t-100) cc_final: 0.8286 (t-100) REVERT: H 344 GLU cc_start: 0.8346 (tt0) cc_final: 0.7948 (pm20) REVERT: H 393 LEU cc_start: 0.8217 (mp) cc_final: 0.7601 (mp) REVERT: H 446 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7899 (ttp-110) REVERT: H 579 PHE cc_start: 0.8080 (t80) cc_final: 0.7806 (t80) REVERT: I 12 TYR cc_start: 0.7536 (t80) cc_final: 0.6990 (t80) REVERT: I 65 LYS cc_start: 0.9164 (tppp) cc_final: 0.8942 (ttmm) REVERT: I 68 PHE cc_start: 0.8470 (m-80) cc_final: 0.8039 (m-80) REVERT: I 76 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7788 (mm-40) REVERT: I 87 GLN cc_start: 0.8593 (pm20) cc_final: 0.8100 (tp40) REVERT: I 91 ASN cc_start: 0.8180 (m-40) cc_final: 0.7884 (m-40) REVERT: J 65 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8679 (mmmt) REVERT: J 74 GLN cc_start: 0.8732 (mt0) cc_final: 0.8171 (mp10) REVERT: M 31 ARG cc_start: 0.7120 (ptp-170) cc_final: 0.6759 (ptp-170) REVERT: M 53 PHE cc_start: 0.8086 (t80) cc_final: 0.7342 (t80) REVERT: M 102 MET cc_start: 0.8834 (ttm) cc_final: 0.8506 (ttm) REVERT: M 150 MET cc_start: 0.7976 (mtp) cc_final: 0.7229 (mtt) REVERT: M 167 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8262 (mpp) REVERT: M 178 TYR cc_start: 0.9139 (m-80) cc_final: 0.7650 (m-80) REVERT: M 196 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8381 (mm-30) REVERT: M 247 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7912 (mt) REVERT: N 19 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8344 (mp) REVERT: N 69 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: N 97 ASP cc_start: 0.8109 (m-30) cc_final: 0.7657 (t0) REVERT: N 123 GLU cc_start: 0.8864 (tp30) cc_final: 0.8223 (tm-30) REVERT: N 147 CYS cc_start: 0.6298 (m) cc_final: 0.6039 (m) REVERT: N 161 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5096 (tt) REVERT: N 175 MET cc_start: 0.7024 (mtm) cc_final: 0.6450 (mtm) outliers start: 92 outliers final: 62 residues processed: 549 average time/residue: 0.1889 time to fit residues: 166.8439 Evaluate side-chains 527 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 453 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP 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 116 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 116 MET 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 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 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 215 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 64 ASN 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 296 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 255 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN H 417 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107836 restraints weight = 66160.344| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.59 r_work: 0.3637 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.9274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28498 Z= 0.203 Angle : 0.782 15.743 39044 Z= 0.392 Chirality : 0.044 0.179 4249 Planarity : 0.005 0.053 4666 Dihedral : 19.899 171.562 5141 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.04 % Favored : 88.54 % Rotamer: Outliers : 3.20 % Allowed : 29.01 % Favored : 67.80 % 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 aren not related in a simple way. whole: -2.82 (0.14), residues: 3081 helix: -0.35 (0.15), residues: 1116 sheet: -2.69 (0.19), residues: 583 loop : -2.79 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 66 TYR 0.025 0.002 TYR M 175 PHE 0.043 0.002 PHE N 14 TRP 0.056 0.002 TRP H 146 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00469 (28498) covalent geometry : angle 0.78159 (39044) hydrogen bonds : bond 0.05757 ( 878) hydrogen bonds : angle 5.39702 ( 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 585 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 500 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7733 (mp10) cc_final: 0.7502 (mp10) REVERT: A 150 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7570 (ptp) REVERT: A 245 LYS cc_start: 0.8543 (mttt) cc_final: 0.8149 (mmtt) REVERT: B 66 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: B 90 GLU cc_start: 0.7761 (tp30) cc_final: 0.7053 (tm-30) REVERT: B 96 GLU cc_start: 0.8136 (tp30) cc_final: 0.7662 (tm-30) REVERT: B 141 MET cc_start: 0.7776 (tpp) cc_final: 0.7191 (tpp) REVERT: B 196 GLU cc_start: 0.8443 (tp30) cc_final: 0.7939 (tm-30) REVERT: C 8 ASP cc_start: 0.8577 (m-30) cc_final: 0.8122 (m-30) REVERT: C 23 ASP cc_start: 0.7514 (t0) cc_final: 0.7219 (t0) REVERT: C 133 PHE cc_start: 0.8378 (m-80) cc_final: 0.8099 (m-10) REVERT: C 167 MET cc_start: 0.7245 (mtm) cc_final: 0.6908 (mtp) REVERT: C 209 MET cc_start: 0.8392 (ptt) cc_final: 0.7831 (ttp) REVERT: D 4 GLU cc_start: 0.7860 (pp20) cc_final: 0.7504 (pm20) REVERT: D 23 ASP cc_start: 0.7748 (t0) cc_final: 0.7531 (t0) REVERT: D 67 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.5962 (mp) REVERT: D 106 TYR cc_start: 0.6934 (m-80) cc_final: 0.6489 (m-80) REVERT: D 141 MET cc_start: 0.7797 (mmt) cc_final: 0.7392 (mmt) REVERT: D 143 LEU cc_start: 0.8943 (mt) cc_final: 0.8677 (mt) REVERT: D 167 MET cc_start: 0.7963 (ttm) cc_final: 0.7624 (ttm) REVERT: D 220 GLN cc_start: 0.8156 (tt0) cc_final: 0.7888 (tt0) REVERT: E 56 MET cc_start: 0.8540 (mtt) cc_final: 0.8101 (mtt) REVERT: E 94 LYS cc_start: 0.7705 (tttp) cc_final: 0.7440 (tttp) REVERT: E 106 TYR cc_start: 0.7073 (m-80) cc_final: 0.6008 (t80) REVERT: E 116 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.5384 (ppp) REVERT: E 208 ASN cc_start: 0.7827 (m110) cc_final: 0.7613 (m-40) REVERT: E 209 MET cc_start: 0.8014 (tmm) cc_final: 0.7230 (tmm) REVERT: E 241 ASP cc_start: 0.8420 (t70) cc_final: 0.8139 (t0) REVERT: E 264 TYR cc_start: 0.1851 (OUTLIER) cc_final: 0.1416 (m-10) REVERT: F 167 MET cc_start: 0.5994 (ptp) cc_final: 0.5604 (ptt) REVERT: F 187 HIS cc_start: 0.7624 (t-170) cc_final: 0.6966 (t-90) REVERT: F 220 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7219 (tm-30) REVERT: G 5 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6923 (mtt-85) REVERT: G 68 PHE cc_start: 0.5830 (m-80) cc_final: 0.5349 (m-80) REVERT: G 107 HIS cc_start: 0.7716 (m-70) cc_final: 0.6312 (m90) REVERT: G 108 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8162 (tm-30) REVERT: H 26 GLU cc_start: 0.7920 (pt0) cc_final: 0.7602 (pt0) REVERT: H 59 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.6728 (mtp-110) REVERT: H 171 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: H 195 CYS cc_start: 0.7834 (m) cc_final: 0.7468 (m) REVERT: H 215 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8252 (m-40) REVERT: H 235 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6824 (tm-30) REVERT: H 289 ILE cc_start: 0.7667 (mm) cc_final: 0.7462 (mt) REVERT: H 342 TRP cc_start: 0.8560 (t-100) cc_final: 0.8234 (t-100) REVERT: H 344 GLU cc_start: 0.8321 (tt0) cc_final: 0.7995 (pm20) REVERT: H 393 LEU cc_start: 0.8251 (mp) cc_final: 0.7977 (mp) REVERT: H 446 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7921 (ttp-110) REVERT: H 579 PHE cc_start: 0.8033 (t80) cc_final: 0.7759 (t80) REVERT: I 12 TYR cc_start: 0.7632 (t80) cc_final: 0.7059 (t80) REVERT: I 38 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: I 65 LYS cc_start: 0.9167 (tppp) cc_final: 0.8953 (ttmm) REVERT: I 68 PHE cc_start: 0.8471 (m-80) cc_final: 0.8021 (m-80) REVERT: I 76 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7796 (mm-40) REVERT: I 87 GLN cc_start: 0.8586 (pm20) cc_final: 0.8046 (tp40) REVERT: I 91 ASN cc_start: 0.8193 (m-40) cc_final: 0.7911 (m-40) REVERT: J 14 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8381 (mp) REVERT: J 65 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8665 (mmmt) REVERT: J 74 GLN cc_start: 0.8719 (mt0) cc_final: 0.8181 (mp10) REVERT: J 124 GLU cc_start: 0.7790 (pm20) cc_final: 0.7433 (pm20) REVERT: M 31 ARG cc_start: 0.7115 (ptp-170) cc_final: 0.6760 (ptp-170) REVERT: M 53 PHE cc_start: 0.8109 (t80) cc_final: 0.7328 (t80) REVERT: M 102 MET cc_start: 0.8848 (ttm) cc_final: 0.8585 (ttm) REVERT: M 150 MET cc_start: 0.7902 (mtp) cc_final: 0.7188 (mtt) REVERT: M 167 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8228 (mpp) REVERT: M 178 TYR cc_start: 0.9139 (m-80) cc_final: 0.7661 (m-80) REVERT: M 196 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8310 (mm-30) REVERT: M 221 MET cc_start: 0.8853 (mmm) cc_final: 0.8508 (mmm) REVERT: M 247 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7900 (mt) REVERT: N 69 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: N 97 ASP cc_start: 0.8095 (m-30) cc_final: 0.7645 (t0) REVERT: N 123 GLU cc_start: 0.8900 (tp30) cc_final: 0.8294 (tm-30) REVERT: N 147 CYS cc_start: 0.6426 (m) cc_final: 0.6070 (m) REVERT: N 161 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5115 (tt) REVERT: N 175 MET cc_start: 0.6949 (mtm) cc_final: 0.6426 (mtt) outliers start: 85 outliers final: 65 residues processed: 554 average time/residue: 0.1923 time to fit residues: 171.4201 Evaluate side-chains 544 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 466 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP 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 116 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 116 MET 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 177 LEU Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 215 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 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 215 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 64 ASN 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: 0.6980 chunk 184 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 231 optimal weight: 0.0670 chunk 175 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN J 91 ASN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.126551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.108390 restraints weight = 65731.984| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.58 r_work: 0.3657 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.9374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28498 Z= 0.187 Angle : 0.776 16.654 39044 Z= 0.388 Chirality : 0.044 0.215 4249 Planarity : 0.004 0.055 4666 Dihedral : 19.892 172.509 5141 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.81 % Favored : 88.80 % Rotamer: Outliers : 3.31 % Allowed : 29.53 % Favored : 67.16 % 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 aren not related in a simple way. whole: -2.78 (0.14), residues: 3081 helix: -0.34 (0.15), residues: 1115 sheet: -2.63 (0.20), residues: 581 loop : -2.75 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 66 TYR 0.029 0.002 TYR M 175 PHE 0.041 0.002 PHE N 14 TRP 0.056 0.002 TRP H 146 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00434 (28498) covalent geometry : angle 0.77559 (39044) hydrogen bonds : bond 0.05696 ( 878) hydrogen bonds : angle 5.37247 ( 2455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6258.55 seconds wall clock time: 108 minutes 52.90 seconds (6532.90 seconds total)