Starting phenix.real_space_refine on Sun Sep 13 11:57:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl0_41358/09_2026/8tl0_41358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl0_41358/09_2026/8tl0_41358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tl0_41358/09_2026/8tl0_41358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl0_41358/09_2026/8tl0_41358.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl0_41358/09_2026/8tl0_41358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl0_41358/09_2026/8tl0_41358.cif" } resolution = 3.1 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= -0.000 sd= 0.018 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 14 5.49 5 S 129 5.16 5 C 14421 2.51 5 N 4281 2.21 5 O 4274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23119 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 28, 'TRANS': 449} Chain breaks: 3 Chain: "B" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3700 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 27, 'TRANS': 449} Chain breaks: 3 Chain: "C" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3678 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 26, 'TRANS': 446} Chain breaks: 3 Chain: "D" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 27, 'TRANS': 450} Chain breaks: 3 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "I" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3711 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 450} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "K" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2084 Classifications: {'peptide': 267} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 250} Chain breaks: 1 Chain: "L" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2089 Classifications: {'peptide': 268} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "N" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.25 Number of scatterers: 23119 At special positions: 0 Unit cell: (108.1, 121.26, 157.92, 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 129 16.00 P 14 15.00 O 4274 8.00 N 4281 7.00 C 14421 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: 1.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 27 sheets defined 40.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.526A pdb=" N VAL A 40 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 removed outlier: 3.870A pdb=" N GLY A 59 " --> pdb=" O ASN A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.525A pdb=" N GLY A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 93 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.711A pdb=" N GLU A 97 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.629A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 230 through 249 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.667A pdb=" N HIS A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.769A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.612A pdb=" N SER A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 447 through 463 removed outlier: 3.726A pdb=" N ILE A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.746A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.723A pdb=" N GLY B 59 " --> pdb=" O ASN B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 70 through 93 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.969A pdb=" N GLU B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.580A pdb=" N PHE B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.516A pdb=" N GLU B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 170 " --> pdb=" O THR B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 170' Processing helix chain 'B' and resid 188 through 199 Processing helix chain 'B' and resid 230 through 249 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.757A pdb=" N GLU B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.613A pdb=" N CYS B 345 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 365 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.684A pdb=" N SER B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 432 Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 466 through 481 removed outlier: 3.667A pdb=" N ALA B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS B 481 " --> pdb=" O GLU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.866A pdb=" N LEU B 511 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 removed outlier: 4.559A pdb=" N THR C 41 " --> pdb=" O CYS C 38 " (cutoff:3.500A) Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 56 through 59 removed outlier: 3.789A pdb=" N GLY C 59 " --> pdb=" O ASN C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 70 through 93 Processing helix chain 'C' and resid 94 through 98 removed outlier: 4.443A pdb=" N GLU C 97 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.577A pdb=" N PHE C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 199 removed outlier: 3.614A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 249 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 262 through 273 removed outlier: 3.690A pdb=" N ALA C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.699A pdb=" N GLY C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.642A pdb=" N GLU C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.546A pdb=" N SER C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 432 Processing helix chain 'C' and resid 447 through 463 removed outlier: 3.527A pdb=" N ILE C 451 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'D' and resid 36 through 41 removed outlier: 3.723A pdb=" N VAL D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 56 through 59 removed outlier: 3.720A pdb=" N GLY D 59 " --> pdb=" O ASN D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 59' Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 70 through 93 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.656A pdb=" N PHE D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.704A pdb=" N ARG D 170 " --> pdb=" O THR D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 230 through 249 Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 262 through 273 removed outlier: 3.551A pdb=" N ILE D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.736A pdb=" N GLU D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 396 through 407 removed outlier: 3.599A pdb=" N SER D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 432 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.502A pdb=" N ILE D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 481 removed outlier: 3.727A pdb=" N HIS D 481 " --> pdb=" O GLU D 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 41 Processing helix chain 'I' and resid 42 through 44 No H-bonds generated for 'chain 'I' and resid 42 through 44' Processing helix chain 'I' and resid 56 through 59 Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 70 through 93 Processing helix chain 'I' and resid 94 through 97 removed outlier: 3.810A pdb=" N GLU I 97 " --> pdb=" O ALA I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 94 through 97' Processing helix chain 'I' and resid 108 through 120 removed outlier: 3.593A pdb=" N PHE I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 200 removed outlier: 3.589A pdb=" N LEU I 192 " --> pdb=" O ASP I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 249 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 262 through 273 Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 324 through 335 Processing helix chain 'I' and resid 338 through 345 Processing helix chain 'I' and resid 354 through 365 Processing helix chain 'I' and resid 395 through 407 Processing helix chain 'I' and resid 425 through 431 Processing helix chain 'I' and resid 450 through 462 removed outlier: 3.909A pdb=" N ALA I 454 " --> pdb=" O SER I 450 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA I 455 " --> pdb=" O ILE I 451 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG I 456 " --> pdb=" O HIS I 452 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR I 458 " --> pdb=" O ALA I 454 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP I 459 " --> pdb=" O ALA I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 481 Processing helix chain 'K' and resid 36 through 44 removed outlier: 3.972A pdb=" N THR K 41 " --> pdb=" O CYS K 38 " (cutoff:3.500A) Proline residue: K 42 - end of helix Processing helix chain 'K' and resid 56 through 59 removed outlier: 4.131A pdb=" N GLY K 59 " --> pdb=" O ASN K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 59' Processing helix chain 'K' and resid 63 through 67 removed outlier: 3.556A pdb=" N GLY K 66 " --> pdb=" O ALA K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 93 Processing helix chain 'K' and resid 94 through 98 removed outlier: 4.416A pdb=" N GLU K 97 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 120 removed outlier: 3.565A pdb=" N PHE K 112 " --> pdb=" O ALA K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 199 removed outlier: 3.917A pdb=" N LEU K 192 " --> pdb=" O ASP K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 243 removed outlier: 3.504A pdb=" N ARG K 243 " --> pdb=" O VAL K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 249 Processing helix chain 'K' and resid 262 through 273 Processing helix chain 'K' and resid 274 through 279 Processing helix chain 'L' and resid 36 through 44 removed outlier: 3.975A pdb=" N THR L 41 " --> pdb=" O CYS L 38 " (cutoff:3.500A) Proline residue: L 42 - end of helix Processing helix chain 'L' and resid 55 through 59 removed outlier: 3.683A pdb=" N GLY L 59 " --> pdb=" O ASN L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 67 removed outlier: 3.559A pdb=" N GLY L 66 " --> pdb=" O ALA L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 Processing helix chain 'L' and resid 108 through 120 removed outlier: 3.648A pdb=" N PHE L 112 " --> pdb=" O ALA L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 199 removed outlier: 3.877A pdb=" N LEU L 192 " --> pdb=" O ASP L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 243 removed outlier: 3.531A pdb=" N ALA L 234 " --> pdb=" O ASP L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 249 Processing helix chain 'L' and resid 262 through 273 removed outlier: 3.556A pdb=" N ILE L 273 " --> pdb=" O VAL L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 279 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.222A pdb=" N TYR A 101 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 128 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 103 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ARG A 130 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 131 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N CYS A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 163 removed outlier: 7.365A pdb=" N MET A 176 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 207 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 178 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER A 209 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TRP A 180 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG A 211 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER A 182 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY A 175 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 255 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 177 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL A 257 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 179 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 259 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 181 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 12.803A pdb=" N ILE A 373 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ARG A 384 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS A 375 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.581A pdb=" N LEU A 370 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN A 420 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 372 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 441 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA A 421 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.255A pdb=" N TYR B 101 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL B 128 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B 103 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ARG B 130 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 163 removed outlier: 7.688A pdb=" N GLY B 175 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N MET B 256 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 177 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 258 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 179 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER B 260 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 181 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AA9, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.507A pdb=" N THR B 312 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 12.788A pdb=" N ILE B 373 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ARG B 384 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS B 375 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.507A pdb=" N THR B 312 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 370 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN B 420 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE B 372 " --> pdb=" O ASN B 420 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 441 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA B 421 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 438 " --> pdb=" O HIS B 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 50 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 163 removed outlier: 7.381A pdb=" N MET C 176 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 207 " --> pdb=" O MET C 176 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA C 178 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER C 209 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TRP C 180 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG C 211 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER C 182 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL C 177 " --> pdb=" O MET C 256 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE C 258 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL C 179 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER C 260 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 181 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL C 259 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE C 286 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 281 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 296 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP C 283 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 294 " --> pdb=" O TRP C 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.877A pdb=" N THR C 441 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA C 421 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 380 through 384 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.472A pdb=" N CYS D 23 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA D 104 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 25 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY D 105 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG D 130 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 163 removed outlier: 7.278A pdb=" N MET D 176 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 207 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA D 178 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER D 209 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP D 180 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG D 211 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER D 182 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 285 through 287 removed outlier: 3.531A pdb=" N GLU D 290 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 350 removed outlier: 12.739A pdb=" N ILE D 373 " --> pdb=" O ARG D 384 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ARG D 384 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N HIS D 375 " --> pdb=" O TYR D 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.990A pdb=" N THR D 441 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA D 421 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 50 through 54 removed outlier: 6.814A pdb=" N GLN I 22 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU I 53 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE I 24 " --> pdb=" O LEU I 53 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY I 105 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG I 130 " --> pdb=" O GLY I 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 204 through 211 removed outlier: 7.689A pdb=" N MET I 176 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE I 207 " --> pdb=" O MET I 176 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA I 178 " --> pdb=" O ILE I 207 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER I 209 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP I 180 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG I 211 " --> pdb=" O TRP I 180 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER I 182 " --> pdb=" O ARG I 211 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL I 259 " --> pdb=" O PRO I 284 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE I 286 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL I 281 " --> pdb=" O GLU I 296 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU I 296 " --> pdb=" O VAL I 281 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP I 283 " --> pdb=" O ALA I 294 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA I 294 " --> pdb=" O TRP I 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 346 through 350 removed outlier: 6.161A pdb=" N ILE I 308 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N CYS I 350 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE I 310 " --> pdb=" O CYS I 350 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG I 307 " --> pdb=" O ILE I 369 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS I 371 " --> pdb=" O ARG I 307 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU I 309 " --> pdb=" O HIS I 371 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE I 373 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA I 311 " --> pdb=" O ILE I 373 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU I 370 " --> pdb=" O VAL I 418 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN I 420 " --> pdb=" O LEU I 370 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE I 372 " --> pdb=" O ASN I 420 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR I 441 " --> pdb=" O LEU I 419 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR I 438 " --> pdb=" O HIS I 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 382 through 384 Processing sheet with id=AC6, first strand: chain 'K' and resid 50 through 54 removed outlier: 3.514A pdb=" N LEU K 53 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS K 23 " --> pdb=" O HIS K 100 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR K 102 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR K 101 " --> pdb=" O THR K 126 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL K 128 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU K 103 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ARG K 130 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 161 through 163 removed outlier: 5.375A pdb=" N MET K 176 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY K 206 " --> pdb=" O MET K 176 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL K 177 " --> pdb=" O MET K 256 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE K 258 " --> pdb=" O VAL K 177 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL K 179 " --> pdb=" O PHE K 258 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER K 260 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL K 181 " --> pdb=" O SER K 260 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU K 255 " --> pdb=" O TRP K 282 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL K 257 " --> pdb=" O PRO K 284 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N PHE K 286 " --> pdb=" O VAL K 257 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N VAL K 259 " --> pdb=" O PHE K 286 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL K 281 " --> pdb=" O GLU K 296 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU K 296 " --> pdb=" O VAL K 281 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP K 283 " --> pdb=" O ALA K 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 50 through 51 removed outlier: 6.267A pdb=" N CYS L 23 " --> pdb=" O TYR L 102 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA L 104 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU L 25 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR L 101 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL L 128 " --> pdb=" O TYR L 101 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU L 103 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ARG L 130 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 161 through 163 removed outlier: 6.676A pdb=" N MET L 176 " --> pdb=" O ALA L 205 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE L 207 " --> pdb=" O MET L 176 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA L 178 " --> pdb=" O ILE L 207 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER L 209 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP L 180 " --> pdb=" O SER L 209 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG L 211 " --> pdb=" O TRP L 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER L 182 " --> pdb=" O ARG L 211 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLY L 175 " --> pdb=" O SER L 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY L 254 " --> pdb=" O GLY L 175 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N TRP L 282 " --> pdb=" O SER L 253 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU L 255 " --> pdb=" O TRP L 282 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL L 257 " --> pdb=" O PRO L 284 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N PHE L 286 " --> pdb=" O VAL L 257 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N VAL L 259 " --> pdb=" O PHE L 286 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL L 281 " --> pdb=" O GLU L 296 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU L 296 " --> pdb=" O VAL L 281 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP L 283 " --> pdb=" O ALA L 294 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 2.52 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: 7927 1.34 - 1.46: 5305 1.46 - 1.58: 10259 1.58 - 1.70: 28 1.70 - 1.82: 181 Bond restraints: 23700 Sorted by residual: bond pdb=" C HIS L 43 " pdb=" N LEU L 44 " ideal model delta sigma weight residual 1.329 1.268 0.061 1.86e-02 2.89e+03 1.07e+01 bond pdb=" CG LYS B 341 " pdb=" CD LYS B 341 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.11e+00 bond pdb=" CG LYS C 121 " pdb=" CD LYS C 121 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.56e+00 bond pdb=" CG LYS D 341 " pdb=" CD LYS D 341 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.19e+00 bond pdb=" CB LYS B 341 " pdb=" CG LYS B 341 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.61e+00 ... (remaining 23695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 31498 2.36 - 4.72: 683 4.72 - 7.08: 88 7.08 - 9.44: 19 9.44 - 11.81: 3 Bond angle restraints: 32291 Sorted by residual: angle pdb=" CG LYS C 121 " pdb=" CD LYS C 121 " pdb=" CE LYS C 121 " ideal model delta sigma weight residual 111.30 99.49 11.81 2.30e+00 1.89e-01 2.63e+01 angle pdb=" N VAL I 381 " pdb=" CA VAL I 381 " pdb=" C VAL I 381 " ideal model delta sigma weight residual 109.30 115.05 -5.75 1.31e+00 5.83e-01 1.93e+01 angle pdb=" C VAL I 40 " pdb=" N THR I 41 " pdb=" CA THR I 41 " ideal model delta sigma weight residual 120.58 126.36 -5.78 1.32e+00 5.74e-01 1.91e+01 angle pdb=" C TYR A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.84 114.45 5.39 1.25e+00 6.40e-01 1.86e+01 angle pdb=" CA LYS B 341 " pdb=" CB LYS B 341 " pdb=" CG LYS B 341 " ideal model delta sigma weight residual 114.10 106.43 7.67 2.00e+00 2.50e-01 1.47e+01 ... (remaining 32286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12774 17.85 - 35.70: 1104 35.70 - 53.56: 179 53.56 - 71.41: 20 71.41 - 89.26: 16 Dihedral angle restraints: 14093 sinusoidal: 5702 harmonic: 8391 Sorted by residual: dihedral pdb=" CA LYS C 121 " pdb=" C LYS C 121 " pdb=" N GLN C 122 " pdb=" CA GLN C 122 " ideal model delta harmonic sigma weight residual 180.00 130.05 49.95 0 5.00e+00 4.00e-02 9.98e+01 dihedral pdb=" CA ASN I 320 " pdb=" C ASN I 320 " pdb=" N PRO I 321 " pdb=" CA PRO I 321 " ideal model delta harmonic sigma weight residual -180.00 -137.81 -42.19 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA LEU I 379 " pdb=" C LEU I 379 " pdb=" N GLY I 380 " pdb=" CA GLY I 380 " ideal model delta harmonic sigma weight residual -180.00 -148.19 -31.81 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 14090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2542 0.048 - 0.096: 730 0.096 - 0.144: 241 0.144 - 0.193: 21 0.193 - 0.241: 3 Chirality restraints: 3537 Sorted by residual: chirality pdb=" CB ILE I 373 " pdb=" CA ILE I 373 " pdb=" CG1 ILE I 373 " pdb=" CG2 ILE I 373 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU A 44 " pdb=" CB LEU A 44 " pdb=" CD1 LEU A 44 " pdb=" CD2 LEU A 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA THR L 41 " pdb=" N THR L 41 " pdb=" C THR L 41 " pdb=" CB THR L 41 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 3534 not shown) Planarity restraints: 4208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 41 " -0.039 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO C 42 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 121 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C LYS C 121 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS C 121 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 122 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 283 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 284 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.030 5.00e-02 4.00e+02 ... (remaining 4205 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3614 2.76 - 3.29: 21497 3.29 - 3.83: 39353 3.83 - 4.36: 44882 4.36 - 4.90: 78402 Nonbonded interactions: 187748 Sorted by model distance: nonbonded pdb=" O ALA A 335 " pdb=" NZ LYS A 341 " model vdw 2.221 3.120 nonbonded pdb=" NH2 ARG B 243 " pdb=" O2' A H 3 " model vdw 2.227 3.120 nonbonded pdb=" NH2 ARG D 243 " pdb=" O2' A E 3 " model vdw 2.242 3.120 nonbonded pdb=" OG SER I 30 " pdb=" OD1 ASP I 32 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR I 377 " pdb=" O LEU I 379 " model vdw 2.259 3.040 ... (remaining 187743 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 21 through 144 or resid 156 through 446 or (resid 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 through 493 or \ resid 505 through 521)) selection = (chain 'B' and (resid 21 through 144 or resid 156 through 446 or (resid 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 through 493 or \ resid 505 through 521)) selection = (chain 'C' and (resid 21 through 446 or (resid 447 and (name N or name CA or nam \ e C or name O or name CB )) or resid 448 through 521)) selection = (chain 'D' and (resid 21 through 144 or resid 156 through 446 or (resid 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 through 493 or \ resid 505 through 521)) selection = (chain 'I' and (resid 21 through 144 or resid 156 through 493 or resid 505 throu \ gh 515)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 21 through 144 or resid 157 through 299)) } 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=0.00 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: 12.890 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.860 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 : 0.007 0.080 23700 Z= 0.329 Angle : 0.841 11.806 32291 Z= 0.483 Chirality : 0.050 0.241 3537 Planarity : 0.005 0.058 4208 Dihedral : 13.377 89.260 8675 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.15), residues: 2878 helix: 0.35 (0.16), residues: 928 sheet: -0.58 (0.20), residues: 690 loop : -1.81 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 243 TYR 0.034 0.002 TYR D 446 PHE 0.016 0.002 PHE D 453 TRP 0.019 0.001 TRP D 282 HIS 0.013 0.001 HIS L 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.33 (23700) covalent geometry : angle 0.84093 / 0.48 (32291) hydrogen bonds : bond 0.17791 / 11.99 ( 947) hydrogen bonds : angle 6.88922 / 4.97 ( 2775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8109 (t70) cc_final: 0.7731 (t0) REVERT: A 251 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8706 (ttm-80) REVERT: B 35 ILE cc_start: 0.9152 (mm) cc_final: 0.8938 (mt) REVERT: B 357 ASP cc_start: 0.8805 (m-30) cc_final: 0.8331 (m-30) REVERT: C 176 MET cc_start: 0.8676 (mtp) cc_final: 0.7834 (mtp) REVERT: D 357 ASP cc_start: 0.9025 (m-30) cc_final: 0.8699 (m-30) REVERT: I 340 ARG cc_start: 0.7719 (mpp-170) cc_final: 0.7503 (mpt180) REVERT: K 87 ASP cc_start: 0.8882 (t70) cc_final: 0.8537 (t0) REVERT: K 142 GLN cc_start: 0.6750 (pm20) cc_final: 0.6085 (pm20) REVERT: K 240 ASN cc_start: 0.7569 (m110) cc_final: 0.7291 (m110) REVERT: K 251 ARG cc_start: 0.7206 (tpm170) cc_final: 0.6695 (tpp-160) REVERT: L 220 THR cc_start: 0.8800 (p) cc_final: 0.8487 (p) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1735 time to fit residues: 54.6246 Evaluate side-chains 163 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 375 HIS ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065626 restraints weight = 55208.632| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.69 r_work: 0.2848 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23700 Z= 0.170 Angle : 0.588 6.688 32291 Z= 0.305 Chirality : 0.043 0.155 3537 Planarity : 0.005 0.060 4208 Dihedral : 5.716 42.712 3474 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.56 % Allowed : 5.89 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 2878 helix: 1.29 (0.17), residues: 954 sheet: -0.55 (0.20), residues: 692 loop : -1.63 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 199 TYR 0.030 0.002 TYR L 114 PHE 0.014 0.001 PHE B 453 TRP 0.011 0.001 TRP B 283 HIS 0.004 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (23700) covalent geometry : angle 0.58804 / 0.31 (32291) hydrogen bonds : bond 0.04514 / 3.06 ( 947) hydrogen bonds : angle 4.99263 / 3.58 ( 2775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8732 (mp0) cc_final: 0.8435 (mp0) REVERT: B 35 ILE cc_start: 0.9126 (mm) cc_final: 0.8917 (mt) REVERT: B 357 ASP cc_start: 0.9049 (m-30) cc_final: 0.8586 (m-30) REVERT: C 176 MET cc_start: 0.9030 (mtp) cc_final: 0.8784 (mtp) REVERT: C 219 ASP cc_start: 0.8934 (p0) cc_final: 0.8545 (p0) REVERT: D 143 ARG cc_start: 0.8110 (tmm-80) cc_final: 0.7657 (ptm-80) REVERT: I 173 GLU cc_start: 0.8730 (tt0) cc_final: 0.8380 (tp30) REVERT: I 176 MET cc_start: 0.8658 (mmt) cc_final: 0.8095 (mmt) REVERT: I 381 VAL cc_start: 0.9001 (t) cc_final: 0.8759 (p) REVERT: K 38 CYS cc_start: 0.8847 (m) cc_final: 0.8560 (m) REVERT: K 87 ASP cc_start: 0.8756 (t70) cc_final: 0.8485 (t0) REVERT: K 142 GLN cc_start: 0.6328 (pm20) cc_final: 0.5847 (pm20) REVERT: K 251 ARG cc_start: 0.6817 (tpm170) cc_final: 0.6317 (tpp-160) REVERT: L 176 MET cc_start: 0.8387 (mtp) cc_final: 0.7756 (ttt) REVERT: L 220 THR cc_start: 0.8826 (p) cc_final: 0.8560 (p) REVERT: L 223 MET cc_start: 0.7937 (ttm) cc_final: 0.7689 (ttm) outliers start: 13 outliers final: 9 residues processed: 190 average time/residue: 0.1671 time to fit residues: 49.4988 Evaluate side-chains 170 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 425 HIS K 22 GLN K 247 ASN L 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064827 restraints weight = 55589.080| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.69 r_work: 0.2834 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23700 Z= 0.188 Angle : 0.555 6.749 32291 Z= 0.287 Chirality : 0.042 0.166 3537 Planarity : 0.004 0.063 4208 Dihedral : 5.383 41.985 3474 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.20 % Allowed : 7.82 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2878 helix: 1.89 (0.17), residues: 949 sheet: -0.51 (0.19), residues: 698 loop : -1.47 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 199 TYR 0.021 0.001 TYR I 446 PHE 0.015 0.001 PHE B 453 TRP 0.010 0.001 TRP C 283 HIS 0.004 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (23700) covalent geometry : angle 0.55535 / 0.29 (32291) hydrogen bonds : bond 0.04080 / 2.79 ( 947) hydrogen bonds : angle 4.61904 / 3.31 ( 2775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8283 (t70) cc_final: 0.7340 (t0) REVERT: B 357 ASP cc_start: 0.9041 (m-30) cc_final: 0.8588 (m-30) REVERT: C 219 ASP cc_start: 0.8948 (p0) cc_final: 0.8604 (p0) REVERT: C 413 GLU cc_start: 0.7857 (tp30) cc_final: 0.7656 (tp30) REVERT: D 143 ARG cc_start: 0.8078 (tmm-80) cc_final: 0.7610 (ptm-80) REVERT: I 173 GLU cc_start: 0.8788 (tt0) cc_final: 0.8413 (tp30) REVERT: I 176 MET cc_start: 0.8601 (mmt) cc_final: 0.8153 (mmt) REVERT: I 381 VAL cc_start: 0.9038 (t) cc_final: 0.8786 (p) REVERT: K 38 CYS cc_start: 0.8828 (m) cc_final: 0.8546 (m) REVERT: K 87 ASP cc_start: 0.8735 (t70) cc_final: 0.8472 (t0) REVERT: K 142 GLN cc_start: 0.6326 (pm20) cc_final: 0.5854 (pm20) REVERT: K 176 MET cc_start: 0.6522 (mtp) cc_final: 0.6013 (mtp) REVERT: K 251 ARG cc_start: 0.6966 (tpm170) cc_final: 0.6482 (tpp-160) REVERT: L 176 MET cc_start: 0.8369 (mtp) cc_final: 0.7112 (mtp) REVERT: L 220 THR cc_start: 0.8777 (p) cc_final: 0.8513 (p) REVERT: L 223 MET cc_start: 0.8354 (ttm) cc_final: 0.7885 (ttp) outliers start: 28 outliers final: 23 residues processed: 180 average time/residue: 0.1675 time to fit residues: 47.1298 Evaluate side-chains 182 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 48 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 234 optimal weight: 0.0670 chunk 243 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 272 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 22 GLN K 247 ASN L 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.089906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066105 restraints weight = 55254.574| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.72 r_work: 0.2860 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23700 Z= 0.114 Angle : 0.504 7.118 32291 Z= 0.261 Chirality : 0.041 0.148 3537 Planarity : 0.004 0.058 4208 Dihedral : 5.226 41.293 3474 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.32 % Allowed : 8.80 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2878 helix: 2.05 (0.17), residues: 952 sheet: -0.51 (0.20), residues: 696 loop : -1.33 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 342 TYR 0.017 0.001 TYR I 446 PHE 0.013 0.001 PHE K 98 TRP 0.010 0.001 TRP D 283 HIS 0.003 0.001 HIS D 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (23700) covalent geometry : angle 0.50388 / 0.26 (32291) hydrogen bonds : bond 0.03501 / 2.40 ( 947) hydrogen bonds : angle 4.40149 / 3.15 ( 2775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8221 (t70) cc_final: 0.7248 (t0) REVERT: B 357 ASP cc_start: 0.9049 (m-30) cc_final: 0.8570 (m-30) REVERT: C 219 ASP cc_start: 0.8909 (p0) cc_final: 0.8580 (p0) REVERT: C 413 GLU cc_start: 0.7877 (tp30) cc_final: 0.7672 (tp30) REVERT: D 143 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7590 (ptm-80) REVERT: I 173 GLU cc_start: 0.8767 (tt0) cc_final: 0.8402 (tp30) REVERT: I 176 MET cc_start: 0.8707 (mmt) cc_final: 0.8276 (mmt) REVERT: I 381 VAL cc_start: 0.9067 (t) cc_final: 0.8796 (p) REVERT: K 38 CYS cc_start: 0.8825 (m) cc_final: 0.8529 (m) REVERT: K 87 ASP cc_start: 0.8733 (t70) cc_final: 0.8471 (t0) REVERT: K 142 GLN cc_start: 0.6360 (pm20) cc_final: 0.5886 (pm20) REVERT: K 251 ARG cc_start: 0.6973 (tpm170) cc_final: 0.6471 (tpp-160) REVERT: L 220 THR cc_start: 0.8841 (p) cc_final: 0.8567 (p) REVERT: L 223 MET cc_start: 0.8451 (ttm) cc_final: 0.7968 (ttp) outliers start: 31 outliers final: 18 residues processed: 183 average time/residue: 0.1678 time to fit residues: 48.0896 Evaluate side-chains 176 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 200 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 22 GLN K 247 ASN L 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.088516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.064793 restraints weight = 55281.404| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.70 r_work: 0.2826 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23700 Z= 0.184 Angle : 0.531 8.990 32291 Z= 0.272 Chirality : 0.042 0.150 3537 Planarity : 0.004 0.063 4208 Dihedral : 5.122 41.172 3474 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.92 % Allowed : 9.61 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2878 helix: 2.24 (0.17), residues: 954 sheet: -0.47 (0.20), residues: 698 loop : -1.27 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.020 0.001 TYR L 101 PHE 0.015 0.001 PHE B 453 TRP 0.009 0.001 TRP D 283 HIS 0.004 0.001 HIS C 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (23700) covalent geometry : angle 0.53054 / 0.27 (32291) hydrogen bonds : bond 0.03655 / 2.51 ( 947) hydrogen bonds : angle 4.34818 / 3.12 ( 2775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8360 (t70) cc_final: 0.7381 (t0) REVERT: B 357 ASP cc_start: 0.9053 (m-30) cc_final: 0.8585 (m-30) REVERT: C 176 MET cc_start: 0.9135 (mtp) cc_final: 0.7886 (mtp) REVERT: C 219 ASP cc_start: 0.8910 (p0) cc_final: 0.8615 (p0) REVERT: C 413 GLU cc_start: 0.7909 (tp30) cc_final: 0.7696 (tp30) REVERT: D 143 ARG cc_start: 0.8039 (tmm-80) cc_final: 0.7637 (ptm-80) REVERT: I 173 GLU cc_start: 0.8810 (tt0) cc_final: 0.8452 (tp30) REVERT: I 176 MET cc_start: 0.8716 (mmt) cc_final: 0.8325 (mmt) REVERT: I 381 VAL cc_start: 0.9112 (t) cc_final: 0.8832 (p) REVERT: K 38 CYS cc_start: 0.8836 (m) cc_final: 0.8542 (m) REVERT: K 87 ASP cc_start: 0.8750 (t70) cc_final: 0.8485 (t0) REVERT: K 142 GLN cc_start: 0.6547 (pm20) cc_final: 0.6053 (pm20) REVERT: K 176 MET cc_start: 0.6566 (mtp) cc_final: 0.6137 (mtp) REVERT: K 251 ARG cc_start: 0.7024 (tpm170) cc_final: 0.6705 (tpp-160) REVERT: L 220 THR cc_start: 0.8872 (p) cc_final: 0.8598 (p) REVERT: L 223 MET cc_start: 0.8519 (ttp) cc_final: 0.8000 (ttp) outliers start: 45 outliers final: 33 residues processed: 183 average time/residue: 0.1597 time to fit residues: 46.0565 Evaluate side-chains 188 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 114 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 HIS I 481 HIS K 22 GLN K 247 ASN L 33 ASN L 56 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065273 restraints weight = 56217.418| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.56 r_work: 0.2773 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 23700 Z= 0.339 Angle : 0.642 7.799 32291 Z= 0.329 Chirality : 0.045 0.155 3537 Planarity : 0.005 0.062 4208 Dihedral : 5.310 43.515 3474 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.01 % Allowed : 10.81 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2878 helix: 2.30 (0.17), residues: 953 sheet: -0.58 (0.20), residues: 703 loop : -1.33 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 46 TYR 0.020 0.002 TYR L 101 PHE 0.025 0.002 PHE B 453 TRP 0.012 0.001 TRP A 180 HIS 0.008 0.001 HIS C 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.34 (23700) covalent geometry : angle 0.64176 / 0.33 (32291) hydrogen bonds : bond 0.04272 / 2.93 ( 947) hydrogen bonds : angle 4.56519 / 3.27 ( 2775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: B 357 ASP cc_start: 0.9055 (m-30) cc_final: 0.8592 (m-30) REVERT: C 219 ASP cc_start: 0.8926 (p0) cc_final: 0.8664 (p0) REVERT: I 173 GLU cc_start: 0.8822 (tt0) cc_final: 0.8467 (tp30) REVERT: I 176 MET cc_start: 0.8679 (mmt) cc_final: 0.8343 (mmt) REVERT: I 381 VAL cc_start: 0.9098 (t) cc_final: 0.8825 (p) REVERT: K 38 CYS cc_start: 0.8858 (m) cc_final: 0.8524 (m) REVERT: K 87 ASP cc_start: 0.8774 (t70) cc_final: 0.8498 (t0) REVERT: K 142 GLN cc_start: 0.6723 (pm20) cc_final: 0.6242 (pm20) REVERT: K 176 MET cc_start: 0.6588 (mtp) cc_final: 0.5987 (mtp) REVERT: K 204 LEU cc_start: 0.8647 (mt) cc_final: 0.8443 (mt) REVERT: K 251 ARG cc_start: 0.7036 (tpm170) cc_final: 0.6666 (tpp-160) REVERT: L 220 THR cc_start: 0.8844 (p) cc_final: 0.8564 (p) REVERT: L 223 MET cc_start: 0.8581 (ttp) cc_final: 0.8305 (ttm) REVERT: L 227 GLU cc_start: 0.8487 (mp0) cc_final: 0.8034 (mp0) outliers start: 47 outliers final: 36 residues processed: 178 average time/residue: 0.1551 time to fit residues: 44.4401 Evaluate side-chains 183 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 224 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS I 33 ASN K 22 GLN K 247 ASN L 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.067641 restraints weight = 55533.088| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.70 r_work: 0.2833 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23700 Z= 0.124 Angle : 0.512 8.563 32291 Z= 0.263 Chirality : 0.041 0.152 3537 Planarity : 0.004 0.058 4208 Dihedral : 5.129 42.847 3474 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.54 % Allowed : 11.49 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2878 helix: 2.38 (0.17), residues: 951 sheet: -0.53 (0.20), residues: 701 loop : -1.24 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 199 TYR 0.014 0.001 TYR L 114 PHE 0.016 0.001 PHE K 98 TRP 0.011 0.001 TRP D 283 HIS 0.003 0.001 HIS B 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (23700) covalent geometry : angle 0.51169 / 0.26 (32291) hydrogen bonds : bond 0.03466 / 2.38 ( 947) hydrogen bonds : angle 4.26145 / 3.06 ( 2775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8257 (t70) cc_final: 0.7235 (t0) REVERT: B 357 ASP cc_start: 0.9032 (m-30) cc_final: 0.8556 (m-30) REVERT: C 176 MET cc_start: 0.9077 (mtp) cc_final: 0.7810 (mtp) REVERT: C 219 ASP cc_start: 0.8881 (p0) cc_final: 0.8589 (p0) REVERT: D 143 ARG cc_start: 0.8031 (tmm-80) cc_final: 0.7468 (ptm-80) REVERT: I 173 GLU cc_start: 0.8754 (tt0) cc_final: 0.8408 (tp30) REVERT: I 176 MET cc_start: 0.8616 (mmt) cc_final: 0.8316 (mmt) REVERT: K 38 CYS cc_start: 0.8804 (m) cc_final: 0.8497 (m) REVERT: K 87 ASP cc_start: 0.8699 (t70) cc_final: 0.8431 (t0) REVERT: K 142 GLN cc_start: 0.6498 (pm20) cc_final: 0.6018 (pm20) REVERT: K 176 MET cc_start: 0.6569 (mtp) cc_final: 0.5994 (mtp) REVERT: K 251 ARG cc_start: 0.6884 (tpm170) cc_final: 0.6504 (tpp-160) REVERT: L 176 MET cc_start: 0.8218 (mtp) cc_final: 0.7910 (mmm) REVERT: L 220 THR cc_start: 0.8795 (p) cc_final: 0.8522 (p) REVERT: L 223 MET cc_start: 0.8562 (ttp) cc_final: 0.8257 (ttm) REVERT: L 227 GLU cc_start: 0.8377 (mp0) cc_final: 0.7947 (mp0) outliers start: 36 outliers final: 31 residues processed: 180 average time/residue: 0.1553 time to fit residues: 44.2817 Evaluate side-chains 181 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 184 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 163 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066011 restraints weight = 54999.409| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.65 r_work: 0.2855 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23700 Z= 0.117 Angle : 0.495 8.926 32291 Z= 0.253 Chirality : 0.041 0.199 3537 Planarity : 0.004 0.058 4208 Dihedral : 4.969 40.984 3474 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.50 % Allowed : 12.00 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2878 helix: 2.41 (0.17), residues: 952 sheet: -0.45 (0.20), residues: 699 loop : -1.18 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.017 0.001 TYR D 458 PHE 0.015 0.001 PHE K 98 TRP 0.010 0.001 TRP D 283 HIS 0.005 0.001 HIS D 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (23700) covalent geometry : angle 0.49454 / 0.25 (32291) hydrogen bonds : bond 0.03247 / 2.23 ( 947) hydrogen bonds : angle 4.15632 / 2.99 ( 2775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8213 (t70) cc_final: 0.7204 (t0) REVERT: B 357 ASP cc_start: 0.9027 (m-30) cc_final: 0.8552 (m-30) REVERT: C 176 MET cc_start: 0.9115 (mtp) cc_final: 0.7827 (mtp) REVERT: C 219 ASP cc_start: 0.8895 (p0) cc_final: 0.8588 (p0) REVERT: D 143 ARG cc_start: 0.8031 (tmm-80) cc_final: 0.7545 (ptm-80) REVERT: I 173 GLU cc_start: 0.8749 (tt0) cc_final: 0.8400 (tp30) REVERT: I 176 MET cc_start: 0.8643 (mmt) cc_final: 0.8329 (mmt) REVERT: I 340 ARG cc_start: 0.7660 (mpt180) cc_final: 0.7454 (mtm-85) REVERT: I 346 GLU cc_start: 0.7758 (mp0) cc_final: 0.7523 (mp0) REVERT: K 38 CYS cc_start: 0.8867 (m) cc_final: 0.8566 (m) REVERT: K 87 ASP cc_start: 0.8710 (t70) cc_final: 0.8441 (t0) REVERT: K 142 GLN cc_start: 0.6539 (pm20) cc_final: 0.6044 (pm20) REVERT: K 176 MET cc_start: 0.6542 (mtp) cc_final: 0.5957 (mtp) REVERT: K 240 ASN cc_start: 0.7324 (m110) cc_final: 0.6991 (m110) REVERT: K 243 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6463 (ptt-90) REVERT: K 251 ARG cc_start: 0.6903 (tpm170) cc_final: 0.6510 (tpp-160) REVERT: L 176 MET cc_start: 0.8224 (mtp) cc_final: 0.7935 (mmm) REVERT: L 220 THR cc_start: 0.8824 (p) cc_final: 0.8557 (p) REVERT: L 223 MET cc_start: 0.8595 (ttp) cc_final: 0.8137 (ttp) REVERT: L 227 GLU cc_start: 0.8355 (mp0) cc_final: 0.7840 (mp0) outliers start: 35 outliers final: 32 residues processed: 181 average time/residue: 0.1675 time to fit residues: 46.9484 Evaluate side-chains 187 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 243 ARG Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 282 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 228 optimal weight: 0.2980 chunk 58 optimal weight: 0.0470 chunk 97 optimal weight: 0.7980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 415 HIS B 425 HIS C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.090421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.066911 restraints weight = 54860.343| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.73 r_work: 0.2866 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23700 Z= 0.097 Angle : 0.487 9.203 32291 Z= 0.249 Chirality : 0.041 0.177 3537 Planarity : 0.004 0.099 4208 Dihedral : 4.913 39.953 3474 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.41 % Allowed : 12.17 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2878 helix: 2.46 (0.17), residues: 950 sheet: -0.33 (0.20), residues: 703 loop : -1.14 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.022 0.001 TYR K 114 PHE 0.016 0.001 PHE K 98 TRP 0.010 0.001 TRP D 283 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (23700) covalent geometry : angle 0.48739 / 0.25 (32291) hydrogen bonds : bond 0.03051 / 2.10 ( 947) hydrogen bonds : angle 4.07492 / 2.93 ( 2775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.774 Fit side-chains REVERT: A 188 ASP cc_start: 0.8135 (t70) cc_final: 0.7149 (t0) REVERT: B 357 ASP cc_start: 0.9008 (m-30) cc_final: 0.8535 (m-30) REVERT: C 176 MET cc_start: 0.9065 (mtp) cc_final: 0.7741 (mtp) REVERT: C 219 ASP cc_start: 0.8890 (p0) cc_final: 0.8559 (p0) REVERT: D 143 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7467 (ptm-80) REVERT: I 173 GLU cc_start: 0.8729 (tt0) cc_final: 0.8373 (tp30) REVERT: I 176 MET cc_start: 0.8599 (mmt) cc_final: 0.8292 (mmt) REVERT: I 340 ARG cc_start: 0.7655 (mpt180) cc_final: 0.7439 (mtm-85) REVERT: I 346 GLU cc_start: 0.7648 (mp0) cc_final: 0.7393 (mp0) REVERT: K 27 LEU cc_start: 0.7676 (mt) cc_final: 0.7427 (mt) REVERT: K 38 CYS cc_start: 0.8836 (m) cc_final: 0.8571 (m) REVERT: K 87 ASP cc_start: 0.8694 (t70) cc_final: 0.8458 (t0) REVERT: K 176 MET cc_start: 0.6556 (mtp) cc_final: 0.5999 (mtp) REVERT: K 240 ASN cc_start: 0.7294 (m110) cc_final: 0.6966 (m110) REVERT: K 243 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6482 (ptt-90) REVERT: K 251 ARG cc_start: 0.6909 (tpm170) cc_final: 0.6524 (tpp-160) REVERT: L 176 MET cc_start: 0.8119 (mtp) cc_final: 0.7836 (mmm) REVERT: L 220 THR cc_start: 0.8794 (p) cc_final: 0.8539 (p) REVERT: L 223 MET cc_start: 0.8586 (ttp) cc_final: 0.8268 (ttp) REVERT: L 227 GLU cc_start: 0.8252 (mp0) cc_final: 0.7830 (mp0) outliers start: 33 outliers final: 27 residues processed: 185 average time/residue: 0.1654 time to fit residues: 48.1516 Evaluate side-chains 185 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 243 ARG Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 221 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065580 restraints weight = 55439.939| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.66 r_work: 0.2851 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23700 Z= 0.166 Angle : 0.516 8.326 32291 Z= 0.261 Chirality : 0.042 0.172 3537 Planarity : 0.004 0.071 4208 Dihedral : 4.871 40.155 3474 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.41 % Allowed : 12.47 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2878 helix: 2.49 (0.17), residues: 950 sheet: -0.39 (0.20), residues: 706 loop : -1.11 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.022 0.001 TYR K 114 PHE 0.016 0.001 PHE K 98 TRP 0.010 0.001 TRP K 77 HIS 0.007 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (23700) covalent geometry : angle 0.51632 / 0.26 (32291) hydrogen bonds : bond 0.03277 / 2.25 ( 947) hydrogen bonds : angle 4.11632 / 2.96 ( 2775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.922 Fit side-chains REVERT: A 188 ASP cc_start: 0.8214 (t70) cc_final: 0.7210 (t0) REVERT: B 357 ASP cc_start: 0.9022 (m-30) cc_final: 0.8536 (m-30) REVERT: C 176 MET cc_start: 0.9067 (mtp) cc_final: 0.7735 (mtp) REVERT: C 219 ASP cc_start: 0.8898 (p0) cc_final: 0.8570 (p0) REVERT: I 173 GLU cc_start: 0.8744 (tt0) cc_final: 0.8389 (tp30) REVERT: I 176 MET cc_start: 0.8583 (mmt) cc_final: 0.8274 (mmt) REVERT: I 340 ARG cc_start: 0.7668 (mpt180) cc_final: 0.7461 (mtm-85) REVERT: I 346 GLU cc_start: 0.7682 (mp0) cc_final: 0.7420 (mp0) REVERT: K 27 LEU cc_start: 0.7777 (mt) cc_final: 0.7513 (mt) REVERT: K 38 CYS cc_start: 0.8872 (m) cc_final: 0.8593 (m) REVERT: K 87 ASP cc_start: 0.8710 (t70) cc_final: 0.8478 (t0) REVERT: K 142 GLN cc_start: 0.7350 (pm20) cc_final: 0.7039 (pm20) REVERT: K 176 MET cc_start: 0.6613 (mtp) cc_final: 0.6007 (mtp) REVERT: K 240 ASN cc_start: 0.7332 (m110) cc_final: 0.6993 (m110) REVERT: K 243 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6518 (ptt-90) REVERT: K 251 ARG cc_start: 0.6887 (tpm170) cc_final: 0.6491 (tpp-160) REVERT: L 161 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7600 (mt-10) REVERT: L 220 THR cc_start: 0.8779 (p) cc_final: 0.8515 (p) REVERT: L 223 MET cc_start: 0.8625 (ttp) cc_final: 0.8219 (ttp) REVERT: L 227 GLU cc_start: 0.8325 (mp0) cc_final: 0.7845 (mp0) outliers start: 33 outliers final: 32 residues processed: 181 average time/residue: 0.1628 time to fit residues: 46.5125 Evaluate side-chains 190 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 243 ARG Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 10 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 265 optimal weight: 0.1980 chunk 207 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065643 restraints weight = 55252.530| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.74 r_work: 0.2838 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 23700 Z= 0.220 Angle : 0.810 59.200 32291 Z= 0.470 Chirality : 0.045 1.081 3537 Planarity : 0.004 0.069 4208 Dihedral : 4.882 40.177 3474 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 1.41 % Allowed : 12.69 % Favored : 85.90 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2878 helix: 2.50 (0.17), residues: 950 sheet: -0.39 (0.20), residues: 706 loop : -1.11 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.020 0.001 TYR K 114 PHE 0.016 0.001 PHE K 98 TRP 0.009 0.001 TRP K 77 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (23700) covalent geometry : angle 0.81042 / 0.47 (32291) hydrogen bonds : bond 0.03245 / 2.23 ( 947) hydrogen bonds : angle 4.11615 / 2.96 ( 2775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4918.84 seconds wall clock time: 85 minutes 27.72 seconds (5127.72 seconds total)